X-Files Mythology Guide Season Three

Mythology Guide: Season Three

THE BLESSING WAY (part 2 of 3)

The Run Down:

Albert narrates: "there is an ancient Indian saying that something lives only as long as the last person who remembers it. My people have come to trust memory over history. Memory, like fire, is radiant and immutable while history serves only those who seek to control it, those who douse the flame of memory in order to put out the dangerous fire of truth. Beware these men for they are dangerous themselves and unwise. Their false history is written in the blood of those who might remember and of those who seek the truth".
Cancer Man and his Army troops beat Albert and his family, demanding to know where Mulder and the files are. Scully goes to the burned out boxcar, but cannot find Mulder. Scully is driving at night when a helicopter forces her to stop. The Army troops search her and take the MJ file printouts, asking for the DAT tape. She says Mulder has it, and they leave.
Back at DC Scully is suspended without pay by Skinner and the OPC Board. She tells them Mulder is dead. Scully tells Skinner the OPC Board is perpetuating a coverup of the people who murdered Bill Mulder and doped Mulder's water. Skinner assures her these men will be brought to justice, she tells him he overestimates his position in the chain of command. Scully checks under Mulder's desk where she hid the DAT tape; it's gone.
The Syndicate Elders, Well-Manicured Man, and Cancer Man meet in their 46th Street NYC Office. First Elder asks about the safeguards, "these files were never meant to be seen". 2nd Elder says "40 years of work, the damage could be incalculable". 3rd Elder says "the damage is done". Cancer Man assures them "we have control", the files are recovered and the stealers have been "removed without incident". There is a small problem in the FBI "but we'll handle that internally as usual". To media it will be nothing but a few scattered obituaries. First Elder asks about "the Mulder problem". Cancer Man says Mulder is dead. First Elder says "then all the pertinent parties should be informed that we can continue with our work".
In New Mexico, the Navajo see buzzards around the boxcar. Albert remembers that as a younger man he like Eric found a Hybrid corpse "at the quarry in a mole, half-buried under rocks, but the buzzards, who will eat anything, would not touch it". In the same hole they find a half-dead Mulder and a Hybrid corpse; Mulder survived the desert heat because he stayed underground immobile. The Navajo take Mulder and prepare a Blessing Way ceremony to heal him, "only the holy people can save [his] life now. he is in their hands".
Frohike visits Scully to show her a newsclipping. The Thinker's body was found in a New Jeresy landfill, killed execution style. The body was discovered after Mulder disapeered. When Scully learns this she says "could they be so stupid?". Scully takes the article to Skinner, suggesting that if the ballistics on The Thinker and Bill Mulder's murders match up then it proves Mulder didn't kill his father. Skinner tears up the article and refuses to look into it. He tells her he was ordered to sign a search warrant on her apartment to look for a DAT tape. She says she doesn't have it and he suggests she brings it to him if she wants anything done. Scully leaves, and Cancer Man comes in from the next room. Skinner says she says she doesn't have the tape, and Cancer Man says "well that's unfortunate for everyone".
In the Blessing Way dreamstate Mulder is visited by the spirit of Deep Throat. Deep Throat mentions "the heavy weight of your burdens which I had once borne". He tells Mulder to go back to life and expose the truth, but also to see justice or else the truth will be a hollow victory. Mulder 'sees' the boxcar. The living Hybrids are huddled inside. Canisters of posion gas (hydrogen cyanide) are thrown in, and the Hybrids desperately seek a way out as they are poisoned to death. Next Bill Mulder visits, to say the lies he told Fox were a poison on his soul, "lies I thought might bury forever a truth I could not live with. [I am] ashamed of the choices I made so long ago, when you were just a boy". He says Samantha is not here, and to go on to find the truth that killed him. Mulder eventually awakens and slowly regains his strength thanks to the Navajo's care.
When going through the FBI metal detector Scully sets it off. They find something metal in her neck; a doctor removes it. There is a tiny scar visible and it can be felt through the skin. Under a microscope, it looks like a highly advanced computer chip. At her sister Missy's urging, Scully undergoes a hypnotic regression about her abduction. She says "there were men, a man took me, there was a light, loud sounds, my ears were pounding, the sound is all screwed up, there was an alarm, they wanted to know if I was alright, I had to trust someone, I was powerless, I could not resist them...". When the doctor puts his hand on hers which is in her lap, she startles awake very afraid. Scully returns home to find Skinner leaving her apartment building. Scully calls Skinner about it, who denies being there in front of Cancer Man. He leaves. That night Scully has a dream where Mulder visits her, saying he's come back from the dead to rejoin her in their crusade for the truth which has put them in great danger.
Bill Mulder's funeral. Scully tells Mrs Mulder that she thinks Mulder is alive. Well-Manicured Man introduces himself to Scully as "a friend of the family" who has to talk to her about "a very serious matter". Well-Manicured Man says he heard her say Mulder is alive, he says he is "a member of a kind of consortium. we represent certain global interests. interests that would be extremely threatened by the digital tape in which you are no longer in possession of, [threatened enough to murder]. He says that Mulder is dead, he's not here to tell her lies, that her life is in danger now too. He says "they'll kill you one of two ways. They'll send someone, possibly two men. They'll kill you in your home or in the garage with an unregistered weapon which will be left at the scene. Using false documents supplied by associates of mine, they'll be out of the country in less than two hours. [Or] he or she will be someone close to you. Someone you trust. They'll arrange a meeting or come to your house unexpectedly". He warns her to stay someone else tonight, they will kill because she wants justice and they are certain she no longer has the DAT tape. He is protecting her because he feels "my colleagues are acting impulsively and your death will draw unnessary attention to our group". She asks what kind of business he's in, he says "we predict the future and the best way to predict the future is to invent it".
Mulder visits his mother at her home. He asks about Bill, about the people he worked with. He finds a picture of some men, including Bill Mulder, Cancer Man, Well Manicured Man, Victor Klemper, Deep Throat, First Elder, 2nd Elder, and 3rd Elder. He asks if they ever came home with Bill, she says yes but she doesn't remember their names. Mulder grabs a gun and tells her he thinks it all has to do with what happened to Samantha. Mrs Mulder is shocked at this.
Scully gets home and is called by Missy, who asks to come over. Another call immeadiately hangs up. Suspicious, Scully calls Missy's home but a machine picks up. Scully leaves a message that she's coming over to her house. She brings her gun and leaves, but finds Skinner outside telling her to get in his car. Skinner takes them to Mulder's apartment which Scully enters with her key. She puts a gun on Skinner. The X signal and bullet hole are still on the window. She accuses him of being sent to kill her. Krychek and Luis Cardinal are waiting in Scully's darkened apartment. Missy comes in the door, and Cardinal shoots her. Krychek sees it isn't Scully and is very distressed. Cardinal leaves the gun with Missy and they flee. Skinner tells Scully if she kills him, she's doing their dirty work and she'll get thrown in prison "there isn't a federal judge they couldn't persuade". Skinner says he came to give her the DAT tape, which is in his pocket. Just then someone arrives at the door. Skinner uses the distraction to pull his gun on Scully.

Plot Points:

Scully is suspended by the OPC Board.
Skinner stole the DAT tape from Scully.
Enter Well-Manicured Man: the superior of Cancer Man and the Syndicate Elders. He feels some of his collegues are acting impulsively with wanton murder, and warns Scully of how they will try to kill her. He claims to be a friend of the Mulder family.
Enter the Syndicate Elders; a group of old men who meet in New York City, often with Well-Mancured Man and Cancer Man. They are worried that exposure of the MJ files will expose their 40 years of work. First Elder in particular dislikes Cancer Man.
Cancer Man must answer to Well-Manicured Man and the Syndicate Elders. He is responsible for seeing FBI matters are handled internally.
The Navajo find Mulder in a tunnel dug by the Hybrids dying of poison seeking escape. They bring him back to live with the Blessing Way ceremony, in which he is 'visited' by Deep Throat and Bill Mulder.
The Thinker has been killed. Skinner is refusing to aid in the investigation or the one concerning Bill Mulder's murder.
Enter the Implant; Scully finds a miniature highly advanced computer chip in her neck which sets off a metal detector.
Scully undergoes hypnotic regression to remember her abduction; there was some kind of an alarm and she reacts with fear when the doctor puts his hand in her lap.
Well-Manicured Man tells Scully about the Syndicate: a consortium representing certain global interests. They are in the business of predicting the future by inventing it.
Well-Manicured Man tells Scully about Syndicate hits: one/two assassins kill the victim with an unmarked gun then leave the country with false papers supplied by the Syndicate. Or, a trusted friend of family member suddenly asks for a meet or shows up at home.
An old picture shows Bill Mulder, Cancer Man, Deep Throat, Well-Manicured Man, Victor Klemper, First Elder, 2nd Elder, 3rd Elder.
Luis Cardinal (with Krychek accompanying) accidently shoot Missy Scully instead of Scully.
According to Skinner, there isn't a federal judge the Syndicate can't persuade.
Scully is approached by Skinner, who has been obeying Cancer Man lately. Skinner says he has the DAT tape but they end up holding guns on each other as someone comes to the door.

Analysis:

Was Cancer Man in the helicopter when the Army troops used it to search Scully? If not, where did he go?
Skinner must have searched Mulder's desk before it ever occured to Cancer Man to do so, so it must have been very soon after Scully first hit the tape there. Scully took it from Mulder when he passed out after witnessing his father's death, she went to the FBI the next day to try and clear him so she must have hid the tape then. How did Skinner manage to keep it hidden from Cancer Man though? And what the hell was Scully thinking hiding it there?! It's the first place people would look!
First Elder mentions safeguards against the MJ documents from ever being exposed; how about not having them on the Internet at all! The only beginning of an excuse for this is Cancer Man saying to Bill Mulder how the computers they only dreamed of have unexpectedly become capable of the best espionage. So the suggestion is that these old fangled 40s men just never thought about the dangers of the Internet, but don't they have advisors to tell them its bad?
Here the Elders say they've done 40 years of work. Thats 1995-40=1955. But in reality the Group/pre-Syndicate began around 1947 maybe earlier. Later this figure becomes 50 years, but its a generalization anyway.
Cancer Man says they handle FBI problems internally as usual. This of course refers to the complete Syndicate infiltration of the FBI, which seems to go all the way to the top. It also hints that Cancer Man essentially serves two functions in the Syndicate; one he runs a cartel of assassins and organizes the clean up crews. Two he handles the FBI. This theory is supported by all the episodes up until "Two Fathers", when suddenly Cancer Man becomes in charge of the Hybrid Program as well!
Notice it is First Elder who brings up the Mulder problem, and who exchanges a tense look with Cancer Man. These two have quite an adversarial relationship, which leads to First Elder trying to kill Cancer Man in "Redux II". This of course also refers to Bill in past tense, perhaps Bill and First Elder were enemies as well.
When the Elders are satisfyed with Cancer Man's report, they say then all pertient parties should be told and the work can continue. From last episode this may be inferred to mean the Italians, Japanese, and Germans though we later learn this isn't so. It more likely refers to the Syndicate facilities (which we learn about in "The Beginning" and "Two Fathers"). It may also refer to the Colonists, though I really doubt they would tell them about this since it would be a show of weakeness.
Cancer Man lies to the Elders, he tells them he retrieved the files which means of course the DAT file as well. Lying is a bad idea here...
So Albert did know about the boxcar full of aliens only because he found it once as a young man. So why didn't he tell anyone?! If he believes in the truth getting out, why not say so? Maybe he was waiting for someone like Mulder who would actually be prepared to do something with the knowledge. This experience probably explains his belief in aliens, though he did call the bodies "lies" so he must know they are not aliens but humans experimented on.
So here's how Mulder escaped death last episode: when the hatch closed and he heard a helicopter coming, he searched around the boxcar for a way out. Finding none, he dived into a pile of mummifyed Hybrid corpes (ugh!). He went for the wall and found that the wall had been clawed through by the desperate Hybrids (how in the hell did they get through the metal door? was there some kind of hatch? If so, why didn't their murderers know of it and seal it? Maybe since the boxcar under ground they figured the hatch would do them any good). He quickly crawled through this tight tunnel full of Hybrid corpses as the Army troops opened the hatch, searched it, then dropped in an incidernary device. It exploded, but the fire didn't get into the tunnel because of the wall of bodies covering the entrance. He then passed out from the heat, and waited in the tunnel until the Navajo found him. In fact, he was so exhausted and weak he couldn't even yell to Scully when she was screaming "MULDER!!" at the boxcar.
When Scully learns the Thinker's body was found after Mulder disapeered she says could they be so stupid? This really doesn't track, what did they do that was so stupid? She later says to Skinner that if the ballistics match on Bill Mulder's and the Thinker's then it will clear Mulder of its his father's murder. First, what are the chances that Krychek would be the one to kill the Thinker too? Surely she thinks the Syndicate has more than one assassin! Second, there's been no mention yet of Mulder being suspected in his father's murder from Skinner or OPC. Third, even if this clears Mulder of his father's murder, the reason he was fired was for punching Skinner! Then again, if she delivers the water filter as evidense that might clear him of that.
Why does Cancer Man make Skinner get an offical search for Scully's apartment? Why not just send one of his assassins?
So Scully hasn't gone through a metal detector in the half-year plus she's been back?! Doesn't she have to go through one to get on an airplane, or does her FBI position preclude her from that?
I don't think these Deep Throat and Bill Mulder visitations were actual spirits, but Mulder's own hallucinations. If these were the real spirits, you'd think they'd tell Mulder the truth about the Colonists and the Syndicate! Same thing for the vision of the Hybrid mass execution; probably Mulder's hallucination.
In the vision Bill Mulder says he's ashamed of the decision he made when Fox was a boy. This means the Syndicate-Colonist alliance of 1973, which suggests he wasn't that troubled about the pre-73 Syndicate stuff, even though we learn otherwise in "Travellers". Even if this is a hallucination of Mulder's, he already knows the "Travellers" information since that story took place in the near past! Then again, the writers didn't know about "Travellers" yet...
Bill Mulder reveals that Samantha is not dead. Mulder already learned this from The Pilot in "End Game"!
Albert warns Mulder about resting after the Blessing Way ceremony, but he immeadiately goes running cross country. But as we see in the next episode, this has no effect on him nor does his bullet wound from last episode!
Most of Scully's regression seems to refer to her inital abduction first by Barry then by the stealth helicopter. She says the sound is all screwed up; this suggests the Stealth Helicopter has some kind of sound dampening system rather than a quieter engine and blades.
Scully says there was an alarm, and people become concerned about her (most likely her fellow abductees like Betsy Hagopian and Penny Northern seen in "Nisei"). Was this alarm related to Scully's Hybrid child ("Christmas Carol" and "Emily") being totally unlike anyother Hybrid clone we've seen birthed from abductees?
Notice that Scully reacts strongly when the doctor puts his hand in her lap. This suggests that something sexual was done to her during her abduction, which we later learn was impregnating her and making her pregnant with a Hybrid fetus.
What exactly was Skinner doing in Scully's apartment? He must have been going through the motions of Cancer Man's order; he already has the DAT tape and he already told her he was ordered to search her apartment.
Scully's dream/vision of Mulder again points to her psychic abilities as in "Beyond the Sea".
The global interests that Well-Manicured Man claim to represent are of course the Colonization by the Colonists.
It's interesting that Well-Manicured seems to trust Cancer Man's word about Mulder being dead over Scully. Perhaps he just thinks she doesn't know anything and is just being hopeful. In any case it should him suspicious of Cancer Man's word now.
In fact, Cancer Man seems to be Well-Manicured Man's only source of information; he says what Cancer Man learns throughout the episode earlier that Scully doesn't have the DAT file and Mulder is dead. This of course suggests that Well-Manicured Man is in constant communication with Well-Manicured Man (at least on a matter this important).
The Syndicate hit meathod two seems to suggest the use of a shapeshifting Pilot in the form of the trusted friend. This doesn't track though; Pilots are only called in by the Syndicate on a vital matter. They don't like calling to help to the Colonists because it is a show of weakness, and because whoever they send will have eyes open and might discover the Syndicate's secret plan of resistance. Maybe it just means they'll grab the person and on threat of death make them call the victim or lead them into a trap.
Well-Manicured Man obviously feels that the murder/disapeerance of an FBI agent would be suspicious and possibly expose the Project, yet this already happened to Mulder. Maybe he's afraid of it happening again.
The collegues that he feels are acting impulsively are obviously Cancer Man who is out to kill anyone who threatens them.
The future the Syndicate is trying to predict is the fate of Earth when the Colonization comes. They predict this future, by collaborating with the Colonists and thus knowing what will happen.
While we later learn that Cancer Man was a close family friend of the Mulders and came over to their house often ("Talitha Cumi"), I find it hard to believe that many if any of the other Elders would be interested in the Mulder family life. Hell, the only reason Cancer Man was there was to screw Bill's wife! Even if they did, Teena Mulder will never tell Fox that.
Teena is obviously shocked to learn that Mulder knows the connection between Samantha's abduction and the Syndicate, since she knows all about it and Bill's connection to it.
What's up with Missy calling like that? It must have been a coincidense, since Krychek and Cardinal were obviously clueless about her. I doubt that after sending a meathod one team Cancer Man would also send a meathod two team with the two teams having no knowledge of the other. Besides, she was concerned about Scully and her regression therapy.
And yes, if you freeze-frame the tape you can definitely see its Cardinal who shoots not Krychek.
It's pretty inept of Krychek and Cardinal to shoot before confirming the identity of the vicitim! It seems like Krychek was senior in position to Cardinal; maybe he ordered Cardinal to fire blind because he knew Missy was coming not Scully, and it was all a plot since he's a Russian Syndicate mole into Cancer Man's operations.
Maybe Skinner was exaggerating when he said there isn't a federal judge the Syndicate couldn't persuade. It's kind of hard to see where he could come across such knowledge, I don't see Cancer Man as being very forthcoming on the subject.
Skinner is there to help Scully. Isn't sticking a gun in her face just worsening an already bad situation? Sure he doesn't like her holding a gun to him, but its overtly suspicious. Then again, we do need a cliffhanger here!

PAPER CLIP (part 3 of 3)

The Run Down:

Mulder breaks in the apartment, ending the standoff between Scully and Skinner. Skinner produces the DAT tape, but refuses to hand it over saying they need to use it as leverage to bring these men to justice. Mulder and Scully leave to find other truths, Skinner keeps the tape. Scully tells Mulder she just knew he was alive and told his mother so. Mrs Scully finds Missy in the hospital; she has a gun shot wound to the head and has been induced into a coma. Albert comes to Missy's bed and says she is weak even through the doctors say she is improving.
Mulder and Scully show The Lone Gunmen the Syndicate photo, they identify Victor Klemper. Mulder says it was taken around 1973. Klemper was part of Operation Paper Clip, bringing German scientists to the US. He experimented on Jews, drowned them, burned them, put them in pressure chambers. He contributed to the space race with knowledge on effects of high altitude flying. Paper Clip officially ended in the 1950s but the scientists continue to live in the US. The Lone Gunmen don't recognize anyone else in the picture.
A Syndicate meeting; Elders, Well-Manicured Man, and Cancer Man. They are alarmed at the Missy shooting and blame Cancer Man and his "ridiculously ineffectual assassins". Cancer Man says "these men are professionals". Well-Manicured Man asks him if he thinks he "can simply fix it with enough bullets". He also says Scully thinks Mulder is alive, but Cancer Man assures them he personally took care of Mulder. They demand to see the DAT tape, he says "I wasn't aware that my honesty was in question or doubt". He says its under security but he can show it to them tomorrow.
Mulder and Scully find Victor Klemper. He says "we were young men caught in a fervor, but our experiments changed the world". Mulder says Bill is dead (who he knew), Klemper says "I believe they would kill anyone if it is in the best interest of the work". Mulder demands the truth but Klemper says "there are some things you don't need to know". Mulder shows him the picture. Klemper asks if they know Napier's Constant and tells them the photo was taken at "the Strughold Mining Company in West Virginia", the rest they can find out themselves. After they leave Klemper calls Well-Manicured Man at the NYC Office. He calls him old friend and says "it's been far to many years". He says the son of one of their collegues visited him. He told the son "that you were the most venal man I've ever met" but nothing else. Well-Manicured Man tells the Elders Mulder is alive. First Elder says "I think its time we call our friends who will handle this matter more satisfactorily".
Skinner contacts Cancer Man, saying he may have the tape but it could fall into the hands of his enemies. Cancer Man is very distressed, demanding he doesn't make deals and he does not negotiate. Skinner says he'll know more when next they meet.
Mulder and Scully visit the abandoned Strughole mine, a factory built into the side of a mountain. They find four high tech security doors. The Napier's Constant code only opens the fourth door. Inside are many long tunnels dug into the mountain, lined with medical filing cabinets, with names in alphabetical order. They're standard medical forms, with birth certificates, smallpox vaccination certificates, and a tissue collection cassette (the new ones are plastic). They start at least at 1955. They check 1964 (Scully's birth year) and find her file with a new tissue collection cassette (and smallpox enoculation certificate). There is one for Samantha, but Mulder's name is under her name label, Mulder asserts the file was originally his. Her tissue collection cassette is new. There is a dull roar, and the power fails. Mulder runs outside to the mine where he sees a bright light lifting off the ground. Outside he sees a large UFO hover away; it is not triangular and has complicated gridwork and lights on the underside. Scully hears a sound and is rushed by several small alien figures. She chases after them, seeing the last of them walk through a door into bright light which then fades. Muder sees a number of black vans pull up outside and non-uniformed troops unload, armed. They see Mulder and shoot at him, he flees into the tunnels, closing the door behind him. The troops know Scully is here too. They enter the code and get through Mulder's door, beginning to search the tunnels for them. Scully leads Mulder to the back door the alien figures used, which they use to escape.
Skinner meets Mulder and Scully. Mulder says the vans the troops arrived in looked like CIA fleet sedans. Skinner says he can negotiate a deal; the DAT tape for their reinstatement into the FBI. They tell him they found an elaborate medical filing system on the American public in a mountain. Mulder wants to keep the tape, Scully wants the deal. She says they're operating outside the law, they can't find justice this way. Scully wants to see her sister, and the truth will only be for Mulder if there is no justice. Skinner tried to make a backup of the DAT tape, but The Thinker put a copy protector on them and a hard copy won't print either. Skinner says they'll have to honor the deal because if they don't, he'll go state's evidense and testify against them so they'd have to kill him too. Mulder lets Scully make the deal with Skinner.
Albert and Mrs Scully sit by Missy's bed. The doctors say she is improving but Albert thinks she will die because for something to live something must be sacrificed. Skinner visits and tells Mrs Scully that Dana is okay. A Suited Man walks by the room again, and Albert tells Skinner this man has been very interested in this room. Skinner chases Suited Man into a stairwell, where he is ambushed by Suited Man, Cardinal, and Krychek. They beat him up and Krychek takes the DAT tape, they flee. Krychek, Cardinal, and a Suited Man later drive up to a gas station. Cardinal and Suited Man go inside. Krychek notices the clock flashing and runs away from the car moments before it explodes. Krychek runs away as Cardinal and Suited Man come out, frustrated that he escaped.
Mulder and Scully return to see Klemper. Instead Well-Manicured Man is there, he says Klemper died of a heart attack. Mulder recognizes him from the photo, Well-Manicured Man says he worked with Bill "since we were young men". Mulder asks about the medical files, Well-Manicured Man tells a story: "In 1947, a spacecraft was reportedly recovered in New Mexico. No doubt you know of this and of the reported recovery of a body at the site. These incidents not only coincided with the end of World War II, but an ignominious project which brought Nazi scientists and war criminals to this country to exploit their knowledge". One of these scientists was Joseph Mengele, who thought he could produce a super-race through genetic engineering. He says Klemper "was able to create some of the most beautiful Hybrids". Mulder asserts Klemper was trying to create an alien-human Hybrid using human test subjects, that's what he saw in the boxcar. Scully doesn't believe it, she says DNA wasn't even discovered until 1944. Well-Manicured Man continues: "When your father realized what the medical data was being used for, he objected strenuously. With the threat of nuclear holocaust in the 1950s, the government instructed men like your father to gather genetic data on the general populous for the purpose of post-apocalyptic identification". Mulder asserts "they took tissue from everyone who received a smallpox enoculation", from hundreds of millions of Americans, so that Klemper "had access to a DNA database of nearly everyone born since 1950". Scully thinks its all a lie to protect human tests, but she can't answer why her file is here. Mulder asserts the current records on file are of abductees, and Scully leaves flustered.
Well-Manicured Man tells Mulder about his sister: "They took her for insurance because your father threatened to exposure the Project. [why not Mulder?] It's not for me to say but your life is in danger now too. You also threaten to expose the Project. You have become your father". He's telling him this because it's what he wants to know. Mulder asks if there's more, he says "more than you'll ever know". He leaves.
Krychek calls Cancer Man at the NYC Office to say he's alive. Cancer Man pretends its good news for the Elders. He asks where he is. Krychek says "somewhere that you will never find me... if I so much as feel your presence, I'm going to make you a very famous man". Krychek hangs up. Cancer Man tells the Elders he just learned the DAT tape has been destroyed in a car bomb which also killed Missy's murderer. First Elder asks about Mulder and Scully. Cancer Man says he has a meeting at the FBI to make a deal, but "there's no deal to make".
Mulder visits his mother. He asks if Bill ever asked her to choose between him and Samantha before she was taken. She says "I couldn't choose! It was your father's choice and I hated him for it. Even in his grave, I hate him still!".
Cancer Man meets Skinner. Skinner offers a deal; the DAT tape in return for Mulder and Scully's safety and reinstatement at the FBI. Cancer Man says he's bluffing, he doesn't have the tape. He threatens him with death by plane crash, botulism, or heart attack. Skinner introduces Albert (Albert says something in Navajo), who has memorized the MJ files and will recite them if anything happens to Mulder and Scully. Albert has taught the information to 20 other Navajo who are throughout the West, so Cancer Man would have to kill every Navajo in the West to keep their quiet. Cancer Man leaves blustered.
Missy died in surgery, the brain damage was worse than they thought. Scully says there is no justice. They have been reinstated in the FBI, and Mulder is sure the truth can be found in the X-Files. Scully says she's heard the truth, now she wants the answers.

Plot Points:

Mulder's Syndicate photo was taken around 1973 at the Strughold Mining Company in West Virgina.
Mulder and Scully meet Victor Klemper; a Nazi doctor brought over by Operation Paper Clip to work with the Syndicate. He experimented on Jews which gave him knowledge of high pressure effects on humans. According to Well-Manicured Man, he was able to create the most beautiful Hybrids. Klemper knew Bill Mulder and Well-Manicured Man, and lead Mulder to the Strughold Mine so he was killed by Well-Manicured Man.
The Syndicate Elders are very angry at Cancer Man and his ineffectual assassins for the Missy Scully shooting. They do not trust him and demand to see the DAT tape. When First Elder learns about Klemper's duplicity, he calls their "friends" who will handle the matter better than Cancer Man.
Enter the Strughold Mine; behind high security doors are tunnels of millions of medical files on American people including smallpox enoculation records and tissue samples (new ones are in plastic). Klemper knew the code for the doors. There is a file for Scully with a recent tissue sample. There is a file for Samantha with a recent tissue sample, with Mulder's name under her label suggesting the file was originally meant for him. Mulder later asserts the recent files were on abductees which Scully denies.
Mulder and Scully visit the mine, Mulder learns his name was under Samantha's files. Armed men storm them and try to kill them, just as a large non-triangular UFO rises off the ground (which Mulder witnesses) and Scully is rushed in the darkness by little alien figures, who disapeer in a flash of light which also shows Scully the way to safety.
Krychek and Cardinal steal the DAT tape from Skinner. Cardinal then tries to blow up Krychek and the DAT tape, but Krychek escapes with the DAT tape. He calls Cancer Man saying he's going into hiding, and if he feels his presence he'll make Cancer Man a very famous man.
Well-Manicured Man meets Mulder and Scully to tell them a story. Nazi scientists were brought over after Roswell to create an alien-human Hybrid. Bill Mulder was part of a government project to collect tissue samples from Americans undergoing smallpox enoculations, but when he learned it was to give Klemper a DNA database to work with he objected. Samantha was taken to ensure he would not expose the Project. There is more, but Mulder will never learn it.
Teena Mulder tells Mulder that it was Bill Mulder's choice to take Samantha, and she hated him for it.
Skinner makes a deal with Cancer Man; Albert and some Navajo have memorized the DAT tape and will reveal it if Mulder and Scully come to harm. They also get reinstated to the FBI.
Missy Scully dies from her gunshot wound to the head after seeming to be recovering.

Analysis:

Mulder would have to be an idiot not to see by now that the Scully family has psychic powers; Missy was able to 'speak' to a comatose Scully in "One Breath", Mrs Scully had a premonition of Scully's abduction in "Ascension", and here Scully has a premonition about Mulder being alive and returning to her.
The Lone Gunmen do not recognize the faces of Cancer Man, Bill Mulder (or maybe they just didn't mention cause Mulder already did), Deep Throat, Well-Manicured Man, and the Syndicate Elders. I guess the Syndicate Elders really have been keeping themselves secret all these years!
This Syndicate-Cancer Man scene in peticular shows us that Cancer Man's job is to run a group of assassins and keep the FBI under control, with perhaps the added responsibility of co-ordinating cover up crews. It also shows us that Well-Manicured Man and the Elders are very disdainful of Cancer Man and his violent assassinating ways. They don't feel all these murders are necessary, and it risks exposure.
It really is curious that these assassins are so shoddy, given that Deep Throat stresses in "The Erlenmeyer Flask" that these men don't make mistakes, and Mulder only survives if they want him to. It's not just Krychek secretly working against the Syndicate either; Cardinal really botches things up in "Apocrypha" too. I guess it's the fault of the writers over anything else, really.
When Klemper says we were young men and our experiments changed the world, he was more likely referring to the Syndicate Project than the Nazi stuff. Their experiments changed the world because it made alien-human Hybrids possible, and thus made Colonization possible!
Klemper obviously does not like Well-Manicured Man (and Well-Manicured Man seems annoyed with him as well). Maybe the Americans had a hard time working alongside Nazi doctors, and that's why Klemper was willing to betray the Syndicate secrets.
Of course, Strughold Mining is named after the leader of the Syndicate, Konrad Strughold (The Movie).
Why does Naiper's Constant only work one of the doors? Why would the other three doors have a different code when once you get through one you have access to all the tunnels since they are interconnected?
Let's talk about the files themselves for a second. For 50 year old filing cabinets in a dank mountain tunnel with puddles of water on the ground, they remarkably look brand new without any rust or mildew! Wow! (This is most likely a production problem).
Wouldn't it be much better to have these files on computer with just a much smaller bank of the physical tissue samples, rather than a mountain full of file cabinets?
First Elder calls "our friends" who will handle the situation better than Cancer Man and his assassins upon learning Mulder is alive and met Klemper. Who are these friends? Given that armed men and tiny alien figures and a large non-triangular UFO show up shortly at Strughold Mining, it could be anyone of these three. Mulder seems to think the armed men (who didn't wear a uniform but blue jackets and jeans) are CIA which suggests Cancer Man probably sent them. Does this mean that their friends are the aliens? If First Elder meant the Colonists, this would be very strange. The Colonists are only to be called when there is a serious alien threat (Faceless Rebels, renegade Hybrids) because first it shows weakness and second when a Pilot is down on Earth then there's a chance he can learn about the Syndicate's secret purpose to find a way to resist the Colonists. However, the armed men have no problem shooting at Mulder with the intent to kill him; Cancer Man doesn't want Mulder killed because he's his pseudo-son, though its possible Cancer Man is so desperate at this point that he will have Mulder killed. And still, those alien figures looked more like Hybrids than Colonists, though the Colonists in "One Son" did have the tiny shape. But why would First Elder want some Hybrids running around there?
And is it just a big raging coincidense that the UFO and the armed men show up at the same time?
It seems like the small alien figures were there to purposely show Scully the escape route; they run past her, she follows them, she sees them exiting out a door where there is a bright light outside. She then uses this door to escape the armed men. This could make it seem that these are the friendly Whiteout aliens of "Little Green Men" and "Fearful Symmetry", yet they look like Hybrids or Colonists and not the elongated alien figure of the one in "Little Green Men".
The alien figures were obviously running outside where a UFO was, which then teleported them up. Was this the same UFO that Mulder saw? Most likely. We never a similar shaped UFO again, so what does that mean? Writers' inconsistancy? The UFO that Mulder sees seems to be lifting off the ground when he first sees it, since the lights go from the ground up. So did the UFO land, drop off those alien figures, then lift up as the alien figures showed Scully the way out, then the now airborne UFO teleported them away then left?
This Strughold Mine sequence is easily the most confusing Mythology Scene EVER.
The Syndicate Elders seem to abhor violence, and Well-Manicured Man doesn't want Scully to die. Yet, it seems very likely that First Elder's "friends" are those armed men who try to shoot Mulder. Do they find Mulder's death acceptible because he knows so much?
Mulder thinks they took tissue during a smallpox enoculation. What does this mean exactly? They took blood with the needle that injected the smallpox enoculation? This would make sense since the person would never notice this. Yet they say tissue, which suggests flesh. Did they scrape some skin off the person? How do they explain this away without being suspicious?
Mulder points out that since Scully's file has a recent tissue container, it means this tissue was taken during her abduction. Yet when he sees Samantha's file with a recent tissue container, he makes no note of it. This means that Samantha is alive and has recently had some tissue removed! And Mulder doesn't seem to notice it!
From what we now know, the Mulder/Samantha name label thing is strange. We know from "One Son" that Bill Mulder had to hand over a child to the Colonists but he refused, changing his mind at the last minute, so the Colonists had to personally come to his house rather than just pick her up at El Rico AFB. We see in "Demons" that Cancer Man apparantly forced Bill and Teena to choose Samantha not Fox, presumably because he saw Fox as his psuedo-son or actual son (he had an affair with Teena). So at what point would the Syndicate make a name label for Fox, then change it at the last minute, not even taking the time to make a new inexpensive folder? This seems like a writers' error to get Mulder to know he was considered for abduction.
Why would The Thinker put a copy protection thingee on the DAT tape?! He wanted the truth to be revealed, so it should follow that he would want to make it easy to make copies! Of course, this is just a big plot contrievance so that Mulder can't keep a hold of this information since it would mean he could actually go public as always so the status quo isn't changed.
Skinner, like last episode, is really overestimating his importance in the chain of command if he thinks the Syndicate will honor the deal over having to kill him! Cancer Man tries to have him assassinated in "Piper Maru"!
Let's see, the files can't be copied or printed but they can be called up on a computer screen. They are in code, but Albert can translate them. How to keep the information after handing over the tape? Why not take pictures of the computer screen, blow them up, and have Albert translate them!
Why would Cancer Man order Cardinal and Suited Man to kill Krychek and destroy the DAT tape? First of all, the Syndicate wanted to see the DAT tape. Cancer Man is getting himself in trouble when he actually has it! This suggests that he doesn't want the Syndicate to see the MJ files, that something bad about him is on it that they don't know about it; yet surely they can access these files! Cancer Man must blame Krychek for the Missy Scully botch, and yet Cardinal was the shooter! Either Cardinal lied to Cancer Man, or Krychek indeed ordered Cardinal to fire blindly at whoever came in the door. Or maybe Cancer Man somehow discovered Krychek was a Russian mole and had to kill him!
Notice Well-Manicured Man doesn't admit to the UFO crash at Roswell, he says it supposedly happened. Deep Throat also told Mulder that Roswell wasn't a big thing, there have been half a dozen better salvages since. This suggests very strongly that Roswell WAS important if these two will stress it to Mulder.
Most of what Well-Manicured Man tells Mulder is a fabrication. He sees to tell Mulder in the hopes of giving Mulder a sense of closure to this saga, so that Mulder will end his little crusade here rather than having to kill Mulder. This of course means that Well-Manicured Man was against First Elder's decision to call his friends (probably the armed men) who then try to kill Mulder and Scully.
If DNA was only discovered three years prior to Roswell, it is pretty fantastic that they could begin genetic engineering so soon. Then again, the pre-73 Hybrids seen in "Anasazi", "731", and "Two Fathers" [in a cut scene] are very crude combinations, seemingly made more from breeding and exposure to radation and diseases than true engineering. This must explain why they allied with the Colonists, because their genetic engineering just wasn't good enough. This means that if the Colonists first appeared in the 1990s and not the 1940s, then the Syndicate would have been able to resist.
So the Strughold Mine medical files work like this; from 1950 to an undisclosed time, the samples are taken from smallpox enoculations. Then, in more recent times, the samples are taken from abductees (who all seem to happen to have smallpox enoculations). Maybe becoming an abductee requires having had a smallpox enoculation (because even if they're given an enoculation there wouldn't be an official certificate). Then again, they look at a few files from the 50s and 60s and decide it's the same for all; maybe abductees without previous enoculations do not have this certificate.
Another lie; Bill Mulder was part of a government effort to catalogue tissue samples from the public. First of all, why would a State Department man do this? Second, Bill was seen in 1953 to be part of the government Group investigating alien appearances.
Well-Manicured Man tries to paint for Mulder a non-alien story of a government conspiracy, which might have technology and tissues from a UFO wreck. In other words, he is leading Mulder directly away from their greatest secret; collaboration with the Colonists.
Another lie; Samantha wasn't taken because Bill threatened to expose the Project; she was taken as part of the exchange of alien fetus for Syndicate Elders' children. Furthermore, Bill never seemed to threaten to expose the Project, he just wanted out. Maybe this lie was also to make Mulder feel guilty for trying to expose the Project by saying he has become his father, who he just learned was party to Nazi genetic experimentation and conspiracies against the American public. Clever.
If he hasn't moved since "Piper Maru", Krychek was in Hong Kong when he called Cancer Man.
Obviously Krychek was threatening to either release the MJ files from the DAT tape (how's he going to do this when Skinner can't?) or release his personal knowledge about Cancer Man.
Considiering how insistant that the Elders were before to see the DAT tape, they inexplicably trust Cancer Man again when he says the file was destroyed! Of course the episode has to end somewhere, but why do they trust his word again?
Teena tells Mulder that Bill chose Samantha. We later seem to learn that Cancer Man decided for them in "Demons". This of course is the reason they got divorced.
Cancer Man claims to be able to make people die of plane crash, botulism, and heart attack. In "S.R. 819" we see Krychek using nano machines to give Skinner a heart attack. It's easy to sabotage a plane, and the Syndicate causes a plane crash in "Tempus Fugit". And botulism is food poisoning, that's easy.
What did Albert say to Cancer Man in Navajo? Cancer Man seemed to recognize the Navajo; does he know the language? He knows German in "Anasazi"!
Skinner seems certain that Cancer Man has the power to reinstate Mulder and Scully in the FBI, and obviously he does. This means he pushed the OPR Board, so they must bow to his power (and he sits in on their meeting in "Ascension") and do take a Syndicate flunkie mind to Mulder matters. Plus, their leader in "Fallen Angel" is shown following Deep Throat's orders and in "Avatar" they had to have been part of Cancer Man's plot to frame Skinner. Then again, in "Herrenvolk" they are interested in Scully's theory on conspiracies against the public so they are not complete stooges, probably more like Skinner is/was.
First Elder arguably tried to kill Mulder and Scully at the Strughold Mine, and when that fails he asks what Cancer Man will do with them. He assures them there's no deal to make at the FBI, and yet he does. So what does he tell the Syndicate when he reinstates them in the FBI? Wouldn't they be very distressed about this? And since he told them the file was destroyed, what does he tell them the deal was about? Why do we never see Cancer Man take any heat on this?
And, Cancer Man seems either non-plused or unaware of First Elder going over Cancer Man's head and calling in their 'friends'.
The death of Missy Scully is very suspicious. The doctors continually say she is improving, but Albert senses she is weak. Then she goes in for surgery, and suddenly the damage is worse than they thought. Add to matters that Suited Man (a Cancer Man hitman) watches Missy's hospital room the whole time. It seems that the doctors were in with Cancer Man, and he made sure that Missy died so she could implicate Cancer Man's failed assassins. Taking Albert's senses as truth, the doctors were lying to Mrs Scully. Plus, after Missy's murder investigation is ceased in "Piper Maru" and Skinner pushes to continue it, he is shot for his interferences. Obviously Cancer Man wants the Missy situation made quiet.

NISEI (part 1 of 2)

The Run Down:

A boxcar 82594 is left alone in a Tennessee trainyard. Later that night 4 Japanese men drive up to the boxcar and are greeted by the Japanese scientist Ishamaru who leaves. These doctors go inside the boxcar, where in a sealed room they operate wearing gas masks on a alien-looking being which has a green blood IV into it. The scientists say "It's heart is stopping now", "look at this deeper part", "how mysterious this is!", "this is good, isn't it?". BlackOps troops wearing gas masks burst into the boxcar and execute the doctors. They put the being in a bodybag and leave. A security camera records the entire event.
Mulder has bought a video copy of the recording from a magazine ad. He says the scientists are extracting green blood from the being, and says its widely held that aliens don't have blood. The seller in Allentown Pennslyvania claims to have pulled it off his satellite dish at night. Mulder and Scully visit the man's house but find the back door busted in, and the man recently shot in the head through a pillow. Mulder finds a Japanese man, Sakurai, fleeing the house, and catches him after a lengthy chase.
Mulder and Scully arrest Sakurai, but Skinner soon arrives and identifies the man as a Japanese diplomat, ordering his release. The murder case will be handled by another agency. Skinner warns Mulder to leave the case and leaves. Mulder shows Scully Sakurai's briefcase which he stole; it contains satellite photos tracking a ship and a list of Allentown MUFON members with the name Betsy Hagopian circled. Mulder leaves for DC to check out the satellite pics and assigns Scully to investigate the MUFON list. Later Sakurai is killed in his limo with a garrotte by Malcom Gerlach, the Red-Haired Man.
Mulder shows the pics to the Lone Gunmen. The satellite used was part American, German, Japanese, and South American. They say the Japanese are very secretive about their spy capabilites and intel data. The pics track the Talapus, a salvage ship out of San Diego. For months it searched for a Japenese sub downed in WWII, rumored to be carrying gold bullion. They claim not to have found it, but the ship went to a Virginia naval shipyard instead of San Diego. Mulder asserts they found something else.
Scully visits Betsy's house, but Penny and Lottie answer instead. They recognize her, saying she is "one of us". They call together their MUFON chapter and say the murdered man was in their MUFON chapter. They all have had an unexplained disapperance they can't remember last year. At the meeting, they say she doesn't remember "the bright white place" because she's only been taken once. They say "there are men there preforming tests" that take their memories away, "but somehow they start to seep back". They suggest regression hypnosis, and say they were all scared at first. Scully has brief flashbacks to her stomach being swelled by some kind of injection. They ask if she has the mark on the back of the neck "where they put the Implants". They all have had theirs removed and carry them around. Scully asks again about Betsy; she's in "the advanced stages if of an undiagnosed cancer ailment. Her body's full of tumors that won't respond to any kind of treatment". Betsy has been abducted repeatedly since her teens, and they tell Scully all abductees will end up like Betsy, "we're all dying because of what they do to us".
Mulder goes to the Virginia naval shipyard. The Talapus refused to be searched when it arrived, but it was soon allowed to dock anyway. It soon left again. Mulder goes searching the shipyard and finds the Talapus abandoned. Soon the BlackOps troops arrive and search the Talapus. Mulder jumps into the sea undetected. At night, ships are searching the sea with spotlights as Mulder sneaks to a brightly lit warehouse heavially guarded by the BlackOps troops. He gets a peek in the window; a large craft is inside obscured by plastic sheets. Many men in hazmat containment suits are hosing the craft with foam. Technicians work machines near it.
Mulder returns to find his apartment ransacked and Skinner waiting inside. Skinner tells him Sakurai was found dead in a canal, and the State Department is harassing Skinner for Sakurai's briefcase; they know Mulder has it. Mulder tells Skinner that Scully has it. Skinner says that this is too big for him to help and leaves. Mulder meets Senator Richard Matheson. He is on "the intelligence committee. Secrets are the only real currency we deal in" and already knows about Mulder's situation. Matheson tells him to return the satellite photos, but Mulder says he can't get stuck in a murder investigation because it will give them time to hide what he just saw. Matheson asks if he trusts him, Mulder doesn't reply. Matheson tells him "the truth": several weeks ago 4 Japanese scientists were murdered in Tennessee, working on a "highly classifyed project". Mulder asks what kind of project, Matheson says "I can't tell you. Some secrets do remain secret, even to me. I was only now just given the names of the murdered scientists". Matheson gives Mulder the 4 names, saying their "past deeds [will] illuminate present treacheries". He says to hurry before he becomes so entagled he can't do anything about it. Mulder asks what this is about, Matheson says "monsters begetting monsters".
Mulder meets Scully at his office. Scully tells him about the dying abductees and her Implant. Mulder gets a fax about the 4 scientists; part of a group of WWII Japanese scientists. Scully recognizes Ishamaru in the picture, but Mudler says he's been dead since '65. "He was the commander of an elite section of the Japanese medical corps know as 731, a unit now known to have experimented on human subjects. [in a cruel manor]... Like their Nazi counterparts, they were never brought to justice". Mulder tells her the 4 scientists were found murdered yesterday. Mulder asserts they were murdered by our government "for continuing their work. The work the Nazis were doing, trying to create an alien-human hybrid". Scully is skeptic, Mulder cites her close encounter in the Strughold Mines and her Implant. Scully says she needs proof. Mulder asserts the Talapus recovered a UFO from the Pacific, and it also recovered an EBE which was autopsied by the Japanese scientists. He gets more satellite pics tracking a boxcar in the fax, and says its "part of our government's secret railroad. Train cars used to carry test subjects".
Scully shows her Implant to FBI Science Crimes tech Agent Pendrell. It looks like "some kind of microprocessor... state of the art. The microlithology's extremely complex. I've never seen anything close to this density". Similar chips can operate via brainwaves "though direct electrochemical interface with the cereberal cortex".
Mulder stakes out a West Virginia trainyard. He sees Japanese men arrive at a certain boxcar and put a small alien-human Hybrid figure in a hazmat containment suit in the boxcar. The Japanese men drive away, and Mulder tries to catch the train but fails. At the Cinncinati train station Gerlach kills the Japanese leader in the bathroom. Isamaru arrives at the station, looking for the dead man. Mulder later arrives, trying and failing to catch the train.
In the X-Files Office Scully watches the alien autopsy tape and sees Ishamaru. She flashes back to her abduction; she remembers seeing 3 masked men standing over her talking in Japanese, including Ishamaru. Scully goes to Mulder's apartment, where X is waiting outside for her. X says Mulder is in danger, "he's tracking a train. You can't let him get on it". X is very distressed and insistant that she warn Mulder not to get on the train. Scully calls Mulder just as he is about to jump on the train from an overpass. She warns him not to get on the train "because they know where you are, and they know what you're doing". Mulder asks who told her, but she won't answer. Mulder jumps on the train anyway, loosing his cellphone.

Plot Points:

Dr Ishamaru co-ordinates a Japanese effort to study alien-human Hybrid bodies, using the Syndicate's secret railroad system of traveling boxcars. The BlackOps troops and an assassin are hunting the Japanese scientists.
These living alien-human Hybrids have a rough alien appearance, are very small, and have the toxic green blood.
A San Diego salvage vessal the Talapus searched the Pacific for a downed Japanese submarine. They instead recovered a UFO which was taken to West Viriginia and guarded by the BlackOps troops.
In Allentown Pennslyvania, a group of repeated abductee women are part of MUFON. They recognize Scully from her abduction. They have all had their neck Implants removed, and their eldest members are dying of a undiagnosed cancer.
Repeated abductee women slowly begin to remember their removed memories and recall a bright white place and men who preform tests on them. A woman only abducted once will remember little.
During Scully's abduction she was worked on by Japanese scientists including Ishamaru.
Mulder contacts Senator Matheson, a member of the Intelligence Committee, who freely offers information on the Japanese scientists but refuses to reveal what they were working on except to say "monsters begetting monsters". Mulder doesn't trust him.
The Japanese scientists are part of 731, a WWII medical unit which preformed horrible medical experiments on POWs.
The Syndicate runs a secret railroad, experimenting on test subjects/abductees in roving boxcars.
The Implant is a highly advanced microprocessor which might react to brainwaves.
Enter Agent Pendrell: an FBI tech in the Science Crimes lab.
X tries to warn Mulder off boarding a train carrying Ishamaru, an assassin, and a living Hybrid through Scully.

Analysis:

So Ishamaru, a Syndicate scientist, somehow managed to sneak off with a living Hybrid in a boxcar. He arranged with his Japanese compatriots to meet there, where his old buddies from 731 would preform a surgery/autopsy on this Hybrid. Ishamaru left when the 731 doctors arrived, presumably to return to his job so he wouldn't be missed. The objective of the 731 scientists seemed to be exploratory surgery to learn about the Hybrid's phyisiology, and also to extract some toxic green blood from it.
Unfortunately for them, a security camera was there to watch and it broadcasted to a satellite. Presumably this is how the BlackOps troops learned about the operation, and moved on it. Unfortunately for them, a man was also able to see the signal on his satellite dish! First of all, weren't there some kind of scrambled signals or anything for security on this transmission? Maybe this guy was a super hacker or something. But didn't Ishamaru know about the camera? Did he never notice it, or did he think he had turned it off? Or was he aware of it, and is playing both sides? Unlikely; Ishamaru's motivation seems to be to sneak Syndicate Hybrid experiment secrets to his homeland.
From this we can infer that the Syndicate has not been sharing its Hybrid secrets with Japan. They seem uneasy allies in "Anasazi", along with the Germans and the Italians. But isn't the Syndicate an international operation, owing allegiance to no country? I suppose this means they don't share their secrets with any country including the USA even though they essentially are the USA.
Apparantly the Hybrid dies in surgery.
Was Mulder just making a joke when he said it's widely held that aliens don't have blood? In a way, he's right; Colonist aliens don't really have blood but Black Oil/Purity running in their veins as seen in The Movie.
For Mulder to have read a magazine ad, and received his tape in the mail, there must have been several days time; for the magazine to be published after the man places the ad, for the magazine to ship, for Mulder's tape to be shipped to him. Yet Sakurai only kills the man right before Mulder arrives there. This suggests that like Mulder the Japanese only learned about the bootleg copy when they bought one themselves. Maybe after this debacle they bought all alien autopsy tapes to find theirs! In any case it's a highly contrived coincidense that Mulder arrives a few minutes after Sakurai.
Sakurai's briefcase showed that Japan has been following Syndicate operations regarding abductions and UFO recovery. Sakurai apparantly wanted to kill Betsy; why? It sounds like he's doing Syndicate dirty work, killing evidense of abductions. Or maybe he wanted to kidnap her so the 731 docs can do some exploratory surgery on her! As for the Talapus, we later learn in "Piper Maru" that it recovered the UFO of a Black Oil alien, and another savage vessal later recovers the Black Oil alien. This whole Talapus thing is not even distantly connected to the abduction/Hybrid programs. Was just a tangent that Japan was interested in, perhaps because the Talapus claimed to be searched for a Japanese sub?
Gerlach seems to represent the same interests as the BlackOps troops; like them he is kiling the Japanese conspirators.
Again West Virginia is a great place to live; apparantly recovered UFOs are taken to its nearby naval yard!
So all those MUFON women were with Scully during her abduction. Isn't this an amazing coincidense, or maybe only Penny and Lottie recognize her. This suggests they were all part of one 'batch'; perhaps these women are abducted at the same time and end up in the same 'batch', and Scully joined their 'batch'. Scully was abducted in Virginia so they were close geographically.
Ironically, by having their Implants removed, the MUFON women killed themselves! We learn in "Redux II" that the Implant is what keeps this unstoppable cancer from devealoping!
Betsy suffers from an undiagnosable cancer, with tumors all over her body. Yet when Scully gets cancer, its only in her nose until "Gethsemane" when the cancer begins to grow into her blood. So the cancer is nasal for a long time, then as the patient is about to die it spreads all over the body. This makes sense, because a year later in "Memento Mori" Betsy is dead.
What were the BlackOps troops doing at the Talapus? Probably searching for Mulder. When that Coast Guard officer found Mulder missing, he must have immeadiately called in the troops. This means that guy was in on it to begin with, so any information he told Mulder is probably a lie. And at night, ships search the sea with spotlights, presumably again for Mulder. And extra BlackOps troops arrive at the warehouse, presumably for Mulder.
As we later see in "Apocrypha", the recovered UFO is a triangular one, a Colonist UFO. The men must have sprayed it with foam because it was radioactive.
The State Department is desperate to get Sakurai's briefcase because they, ie the Syndicate, are desperate to learn what Japan knows. The BlackOps troops probably ransacked Mulder's apartment looking for it.
Matheson is definitely a Syndicate pawn here. First of all, he feels free to talk when in "Little Green Men" he had to whisper and blare music in his office. Second, he suddenly has all this information for Mulder that will set him off to track down the Japanese conspirators (thus doing the Syndicate's footwork) yet gives him nothing concerning the Syndicate project which Japan is after. Notice how he says he was only just given the names of the murdered docs, presumably by the Syndicate because they knew Mulder would go to Matheson next. The only time he ever seem to be actually helping Mulder is when he tells him its about monsters begetting monsters, which means the Axis scientists creating unnatural alien-human Hybrids.
If Ishamaru's death was faked in '65, then presumably that is when he went to work for the Syndicate. Then again the Axis scientists were brought over in the late '40s so maybe this was when he got promoted to head Hybrid project guy.
So Matheson informed Mulder about the secret railroad, even telling him which boxcar the Japanese would next use. While this is risky, it must have been done so Mulder could intercept the next attempted Hybrid autopsy/surgery/kidnapping or at least discover it for the Syndicate and/or BlackOps.
In this episode the Implant is a computer chip which reacts to brainwaves, thoughts. In later episodes we learn it retards nasal post-abduction cancer and can cause the host to be drawn to an abduction 'lighthouse'. This whole mind-reading thing seems to have been dropped, but then again maybe its connected to the 'lighthouse' function. Maybe instead of reading thoughts it forces thoughts on the host, as in go to this 'lighthouse'.
The living Hybrid that the Japanese take into the boxcar is very co-operative. As we later learn, these 'Hybrids' are actually humans that have been experimented on and are terrified of the soldiers who come to massacre them. Yet this one willingly goes along with the Japanese; assuming these people are still able to think and communicate maybe Ishamaru promised him freedom if he came along with him, and maybe that's how Ishamaru absconed with the other one at the beginning of the episode.
Why is this Hybrid in a containment suit? It suggests that he breathes a different atmosphere, yet the Hybrids in the next episode breath air just fine. Perhaps it was prevention against contanimation from the toxic blood for the Japanese.
It seems that Gerlach killed Ishamaru's bodyguard/contact, so that he would board the train alone and be vunerable.
Scully sees Ishamaru in the autopsy tape, yet he left before it began. Perhaps she is looking at the tape before the other docs arrive and Ishamaru is waiting inside the boxcar for them.
X obviously doesn't want Mulder on that train. Why? If its because X is a true Syndicate man, then its to prevent Mulder from getting evidense in the form of the Hybrid and/or Ishamaru. If its because X is Mulder's ally, then its to prevent Gerlach from killing Mulder as he tries to do next episode. But wait! Cancer Man's assassins and clean up crews seem to have standing orders to let Mulder live, as we see time and time again. Gerlach's willingness to kill Mulder suggests he is not allied with Cancer Man, and his actions which seem in co-ordination with the BlackOps troops thus suggests that BlackOps is not allied with Cancer Man, or at the least they disagree on some things like letting Mulder live. We later see that X handed over Ishamaru's journals on the train to Cancer Man; perhaps Cancer Man was aware of this mini BlackOps v. Japan war and sent X to make sure Mulder doesn't killed by it, even though he's being used as a Syndicate scout here.
Scully says to Mulder that "they" know where he is and what's he's doing, so she seems to associate X with the Syndicate already.

731 (part 2 of 2)

The Run Down:

Hansen's Disease Research Facuilty, West Virginia: military troops storm the center, breaking through the gated entrance. They round up living Hybrids who can't speak only meow and then execute them all, burying them in a mass grave. A fightened leper Escalante watches and escapes detection.
Scully asks X about the Japanese and Ishamaru, what's on the train. X says he doesn't know, "there are limits to my knowledge". X tells her if she wants to know what's on the train and who killed her sister, then find out about the neck Implant. "It holds more than I could ever tell you. Maybe everything you need to know". X leaves. Scully has Pendrell work on the Implant; its neural network stores biological information from electrical impulses. By being in the neck, it may be "replicating the memory process in the brain. This kind of neural network could not only be collecting information, but artificially replicating a person's mental processes". Scully summarizes that you could know a person's every thought. Such a complicated neural net has never been seen before, but it was destroyed by Pendrell's testing because it was so delicate. A Japanese manufacturer's name is on the silicon matrix, but the only evidense of such a manufacturer is in a single shipment to a Dr Zama at the Hansens West Virginia Facuilty. Pendrell likes Scully.
Mulder gets on the train but can't get into the 'quarantine' boxcar, there is a locked security door. The Conductor doesn't have access to them, "we pick them up from time to time. Whatever they're carrying they never let us know". Ishamaru is travelling under the name Zama; in his room are journals in Japanese which Mulder gives to the Conductor. Elsewhere, Gerlach executes Ishamaru/Zama with a garotte.
Scully travels to the Hansen's Facuilty and finds Escalante and other lepers hiding. They say the center is closed now, Zama and the medical staff left just before the death squads started arriving. Hundreds have been killed, but they weren't lepers; they began arriving several years ago and they were kept seperate. "They had Hansen's deformities. Dr Zama would round them up in groups for treatment. And then the ones that returned always came back worse, with terrible burns all over their bodies". Military troops arrive again in a helicopter; they catch Scully and execute Escalante.
Mulder discovers Ishamaru's body and the 'quarantine' boxcar security door unlocked. At the back is a sealed room, with a frightened alien-human Hybrid inside. Mulder is attacked by Gerlach and choked with the garotte. The Conductor stops Gerlach and seals the two of them in the boxcar. Mulder now has his gun on Gerlach. Gerlach demands to know who Mulder is, he has a National Security Agency badge. Gerlach says there's a bomb on the train, activated by him opening the door, "because of what's in that room. Because if the man responsible couldn't get it out of the country, he would rather kill it than let it live". Gerlach says Zama gave him the access code just before he killed him, but that code would surely detonate the bomb on exit because Zama knew he was going to die.
Scully is taken to First Elder, who says "I know most everything about you, Dana". First Elder says the lepers were killed because they "had been exposed [to] the same thing all these victims had been exposed to, victims of an inhuman project run by a man named Zama". Scully says he's the Paper Clip scientist Ishamaru, First Elder says the ruler of the world has the best scientists not soldiers now. "Unfortunately, Ishamaru began to conduct his work in secret, not sharing with those who had risked much in giving him asylum". He exposed the lepers to "terrible things" to which Scully might have been exposed to, he doesn't know.
First Elder takes Scully to a mothballed 'quarantine' boxcar in West Virignia. First Elder calls Gerlach, who gives his phone to Mulder to he can talk to Scully. Scully says Ishamaru Zama was "experimenting on human test subjects. He'd been doing it for years, operating out of a leper colony. The leper colony was just a front. The tests weren't on lepers, they were on the homeless, the insane, they were brought here and they were subjected to diseases and radiation tests". Scully believes First Elder because of the boxcar she's in; "this is where they brought me. This is where they put the Implant in my neck, in one of these cars... Ishamaru Zama was using the secret railroad to conduct his tests across the country. The women in Allentown, they all remember these cars". She says it means that alien abductions are a government coverup to their operations, and the UFO Mulder saw was a piece of a raised Russian nuclear sub. She says two weeks ago the President apologized for "secret radiation tests that had been conducted on innocent civilians up until 1974". But those tests never ended. The boxcar bomb will expose thousands to hemorragic fever, what that test subject in back had been exposed to. Scully tells him where the bomb is, and says "they" want him to stop at the next station so they can get a bomb squad out there. Mulder hangs up, and gets the Conductor to reroute the train to a secluded area then unhook the 'quarantine' boxcar. Gerlach says "they'll never be able to find us in time". Mulder is confident the test subject is too important to loose.
Mulder asks Gerlach about his orders. Gerlach says "they don't make provisions for saving my life". He doesn't know about saving the test subject because he wasn't expected to fail. On some threatening, Gerlach says what the test subject is; "it's a weapon". What could be better than Star Wars, atomic bombs, or advanced biological weapons? Mulder asserts "a standing army immune to the effects of those weapons. That's what Dr Zama did, didn't he? He came up with an immunity to those weapons, and he was trying to smuggle that thing back to his own country to share the science, only our government isn't in the mood to share, right? They've been doing experiments since WWII, tests on innocent civilians, but Zama succeeded where the others had failed. And that thing in there... It's an alien-human Hybrid isn't it? Gerlach says if that were true, someone would come to save it.
Scully tries to call Senator Matheson but can't reach him. She also puts the X Signal on Mulder's apartment window. Watching Mulder's alien autopsy tape, she gets the exit code when Ishamaru leaves. Mulder uses the code to open the door, but Gerlach attacks him, knocking him out. Gerlach leaves, but gets shot and soon dies. X steps in, checking Mulder. He walks over to the rear room, trying unsuccessfully to wrench open the locked door. After a moment's indecision, he leaves with Mulder's body. The bomb detonates, destroying the boxcar in a large explosion.
A week later, the boxcar has disapeered and Matheson is out of the country, refusing to return Mulder's calls. Mulder was found injured when someone in a phonebooth alerted the nearby hospital of Mulder's location. Zama's briefcase has been returned, but its a fake one with fake papers. The bodies at the Hansen's Center have disapeered. Scully says that Mulder is helping them create an alien cover story to hide their true deeds, and they apologize for what they can't hide, "apology has become policy".
Somewhere, a Japanese man is translating Ishamaru's papers, while Cancer Man watches.

Plot Points:

X tells Scully her Implant is the key to everything.
The Implant is a neural network which might be able to record the host's thoughts. It was made by an unheard of Japanese manufacturer. A single shipment was sent to Ishamaru's leper research center.
Trains regularly pickup the 'quarantine' boxcars but don't have access to them.
Ishamaru worked in a leper medical research center in West Virginia, where the insane and homeless would be brought in and given treatments which only worsened their condition. According to First Elder, they were exposed to diseases like hemorragic fever and radation treatments. Now military troops are executing these alien-looking creatures who can't talk.
Ishamaru began to work in secret and not share his knowledge with the Syndicate.
Ishamaru was killed by an assassin while trying to smuggle a alien-human Hybrid out of the country.
First Elder meets Scully, and claims to know everything about her.
Scully and the Allentown women all remember the 'quarantine' boxcars from their abductions.
Secret radiation tests were conducted on the unwitting public until 1974.
According to the assassin, the Hybrid is a weapon immune to biological weapons and radiation. Ishamaru is the only one to suceed.
Senator Matheson avoids getting involved with Mulder concerning this.
X saves Mulder's life after killing the assassin and trying to save the Hybrid.
Cancer Man now has Ishamaru's medical papers.

Analysis:

Military troops execute the Hybrids at the center, not the BlackOps troops who chase Mulder and guard the UFO and kill the Japanese scientists. Is there any importance to this?
According to Escalante, the death squads have come several times. Yet in the opening the troops bust through a gated fence. Apparantly Ishamaru and his medical staff went AWOL from the center, and then the death squads arrived since Ishamaru's duplicity had been revealed. So who gated up the fence again if the lepers and Hybrids were abandoned? Did the lepers do it?
These Hybrid creatures have a rough alien appearance including elongated hands and an altered skull. Strangest of all, they can't talk and only make a soft sound like a meowing cat!
If the death squads have come before, why didn't the Hybrids hide like the lepers? Perhaps the treatments have made them mentally retarded or something like that, so they're not really aware of the world around them.
After Pendrell's tech speech, Scully summarizes that the Implant could record thoughts. Yet Pendrell said it "could not only be collecting information, but artificially replicating a person's mental processes". To me that sounds like not only can it record thoughts, but it can artificially impose false memories into the brain! Is this a version of the memory wipe they use for abductions? Unlikely, because in "Deep Throat" we see them use a simple injection (and in "Jose Chung" a hypnotist is also involved).
Knowing what we now know from "One Son", this whole Ishamaru/Hybrid thing takes a completely different meaning. In "One Son" we learn that prior to the Syndicate-Colonist Alliance of '74, the Syndicate did crude experiments to create an alien-human Hybrid but failed miserably. It seems that the crude Hybrids and boxcars seen in "Anasazi", "Nisei", and here are evidense of that pre-'74 Syndicate experiment time. Apparantly from Roswell '47 they got alien technology but not alien tissue; in '74 they got the all important alien fetus which gave them the alien genome. If so, what were they crossing humans with in the pre-'74 era? Maybe they had alien bodies from wreakages but they missed something or more likely their technology wasn't advanced enough to do true gene-splicing or something like that. So the Axis scientists like Ishamaru and Klemper ("Paper Clip") were brought over to work on the alien-human Hybrid project. Ishamaru didn't seem to use alien tissue at all, merely radiation and diseases, the same might have gone for Klemper. Yet in '52 in "Travellers" the Syndicate does a crude grafting of some living alien creature to a human.
In any case, it seems that Ishamaru's Hybrids were non-alien. This explains why First Elder was so forthcoming about it to Scully; it perpetuates the Syndicate's coverstory that there are no aliens just an evil government, thus further concealing their greatest secret of Syndicate-Colonist collaboration.
Yet Ishamaru was still working with the Syndicate last year when Scully was abducted. So he must have still been working on the Hybrid project after '74 when they got the alien genome. Another inconsistancy; Escalante said the Hybrids only began to arrive "several years ago". Now, Escalante looks roughly 30-40 so at the earliest he's been at the center since @'55. Several years doesn't sound like decades, it sounds like only a handful of years. Then again, perhaps Ishamaru worked at a different center earlier and then "several years ago" he came to this one and along with him came the Hybrid experiments.
The only recorded Implant shipment was sent to the center for Ishamaru. This suggests that he's running the local abduction operations in addition to these crude Hybrid tests. Sure he worked on Scully, but if he's doing these advanced abduction operations why would he still continue with these primative tests? It doesn't make sense. Perhaps this is a writers inconsistancy.
So Ishamaru worked for the Syndicate trying to make a Hybrid. The Syndicate refused to share his research with Japan, apparantly this was part of an agreement with the Syndicate and other countries, perhaps only with the Axis countries from which they took the scientists (why explains the Axis countries' animostity towards the Syndicate in "Anasazi"!). So Ishamaru decides to grab some Hybrid information and defect to Japan. First he grabs a living Hybrid and his friends do an autopsy on it; they get blown away by BlackOps. Then he steals another living Hybrid, and just tries to flee the country with it using the Syndicate's secret railroad. But the two different Hybrids stolen look different; in fact the first one looked more like the Hybrids in "Ansazi" (Klemper's Hybrids?) and had the alien blood so perhaps it was a more modern one, then Ishamaru had to settle with one of his crappy Hybrids cause the heat was on.
What's up with First Elder's intimate declaration that he knows everything about Scully, even calling her by her first name? The implication was that First Elder watched over her during her abduction, but in "One Son" we learn that Cancer Man is in charge of the abduction operations. This strange concern for her promptly disapeered; in The Movie he's all for killing her!
As I understand it, Zama is the false name for Ishamaru. So when Gerlach and First Elder call him Zama, it means they're lying. So most of what First Elder says is questionable; thought most of it makes sense!
First Elder doesn't know if Scully has been exposed to Ishamaru's "terrible things". Sounds like Ishamaru was working on abductees but the Syndicate didn't have a very tight grip on him, and isn't sure if he was subjecting the abductees to his horrors.
The fact that First Elder knows Gerlach's phone number obviously suggests that he sent him. If Gerlach truely is with the NSA, then it means the Syndicate has infiltrated the NSA as well.
How does Scully know that the Allentown women remember a boxcar if she just learned herself? Sounds like she's assuming here.
How can Scully believe that the recovered wreakage was a Russian sub?! They went looking for a Japanese sub, and look who's she talking to! Shouldn't she be more skeptical, even if some of what he says is the truth?
So the US conducted secret radiation tests until 1974. This makes sense; in the pre-'74 era the Syndicate was forced to use things like radiation trying to make a Hybrid, but in '74 they got the alien genome so they didn't need the radiation tets anymore! So Scully and Mulder assume incorrectly when they say the tests have continued; they don't need to.
First Elder tells Scully the bomb will release hemorragic fever; it doesn't. Yet she still seems to trust what he told her!
Notice how First Elder tries to talk Scully into talking Mulder into stopping the train so they can get there and steal the Hybrid, because its evidense against them.
Of course, Gerlach's whole story about the Hybrid being a weapon immune to biological weapons and radiation is a fluff story, but then again it does indirectly carry a certain truth. The purpose of Hybrids to be immune to the Black Oil, which is arguably a disease which is radioactive! It's doubtful that Gerlach knows the real truth though, he's just an assassin.
Matheson proves he is a Syndicate stoodge; he refuses to help Mulder here when before he was so helpful because now Mulder saw more than he was supposed to.
X's actions could mean several things. The obvious explanation; he shows he is truely Mulder's ally by risking exposure to come and save his life. Or, he shows he is a truely loyal to Cancer Man by following his orders to rescue Mulder, his pseudo-son who he doesn't want to die. Or, he came to get the Hybrid on Cancer Man's orders but it was locked in so he saved Mulder. Or, he came to get the Hybrid on Cancer Man's orders but instead saved Mulder.
The boxcar that Mulder spends the episode in has a satellite dish on top like the last one. Does this mean his entire experience inside was broadcasted, and that X's subsequent rescue of him was also broadcasted?
Remember its very likely that a security camera recorded the events of the boxcar. This probably means that X was just following orders by killing Gerlach, trying to rescue the Hybrid, then rescuing Mulder. If he didn't, then whoever was watching that satellite feed saw X's betrayal of the Syndicate, and X would have been held accountable. However, this might have happened! In "Herrenvolk", approximately half a year from now, First Elder tells they have an information leak; it is ultimately revealed to be X. But we never see how First Elder learned this; perhaps he learned it here. Then again, would he sit on it for a half a year? Supporting this is that X doesn't appear again until the end of the year.
And if X was following orders in killing Gerlach, it could mean two things. One, Gerlach failed in his assignment and was thus killed, just like Krychek was almost killed in "Paper Clip" for his failure to kill Scully. Or, he was killed as part of a rivalry between Cancer Man and the NAS/BlackOps. Gerlach seems associated with the BlackOps in that their actions compliment each other, and in "Paper Clip" we see First Elder calling in (maybe, it's unclear) BlackOps when Cancer Man's assassins fail to do the job. We also see repeatedly a Cancer Man - First Elder rivalry. And here wee see First Elder and Gerlach associated. So perhaps Cancer Man was kept out of these events at first while First Elder and his BlackOps and Gerlach handled the situation. Then Cancer Man got involved, getting X to try and warn Mulder off the train because he knew a rival assassin was there who would kill Mulder unlike the Cancer Man assassins. So X killed the BlackOps/First Elder assassin because of their rivalry, which means X was just following Cancer Man's orders here.
Obviously X contacted the nearby hospital so it'd pick up Mulder for treatment.
So the Zama briefcase was switched. Last we saw it, Mulder gave it to the Conductor and then the Conductor went on with the train why Mulder was left behind in the boxcar. So at the next train station, some Cancer Man assassin grabbed the briefcase from the Conductor and gave it to Cancer Man.
Why exactly are these papers Ishamaru wrote? Presumably they're research notes on Hybrid experiments, things that Ishamaru had been keeping secret from the Syndicate recently, so it more likely involves the modern Hybrid/abduction operations.

PIPER MARU (part 1 of 2)

The Run Down:

Pacific Ocean: the French salvage ship Piper Maru sends Gautier into the water in a heavy dive suit. They have been searching for three months, and now detect a large amount of radiation. Gautier finds a sunken airplane, which they call "one of the squadron". Gautier looses contact with the surface, and he finds a living human inside the air-filled cockpit, banging on the glass. The human has Black Oil running through his eyes. Later the crew pull up Gautier, his suit covered with an oily substance. Gautier says he's fine, but the Black Oil is running through his eyes.
Skinner tells Scully that Missy's murder investigation has been ceased 5 months after the fact. Skinner says he's going to appeal the decision, that it is nothing suspicious, but Scully says it is suspicious that they can't find any facts.
Mulder tells Scully how the Piper Maru limped into port at San Diego, the entire crew is being treated for radiation burns. The French government is keeping why classified. Using satellite pics Mulder tracked its original position to the same place where the Talapus retrieved a UFO ("Nisei"). They go to San Diego and visit the hospital. The doc says they have "somatic" symptoms, but the effects are degrading rapidly. They suffer severe delirium. They were exposed to radiation levels approaching Hiroshima. Gautier was the only one unaffected by the radiation and piloted the boat in. He was in very good health and his "leukocytes and erythocytes" were high. He checked himself out. The Piper Maru has no radiation levels at all. Mulder finds Gautier's oily heavy dive suit and Scully finds a ocean map with the name "Zeus Faber" marked on it. The place has been ransacked. Reviewing the dive tape, Scully identifies the sunken airplane as a WWII era P-51 Mustang fighter. She gets the identication number and leaves to see someone for information.
Gautier arrives at his house and proceeds to ransack it. Later Mrs Gautier comes home to find her husband, who eyes her coldly. He grabs her as the Black Oil runs through his eyes. Later Mrs Gautier leaves the house, with the Black Oil running through her eyes. Mulder arrives later to find a letter in French about salvage and with the P-51's ID number. The letter's return address is Kallenchuk Salvage Brokers in San Francisco. Mulder takes the letter and finds a disoriented Gautier on the floor covered in an oily substance. When Mulder asks about Kallenchuk, he refuses to answer and demands to speak with the French Consul General.
Scully visits an Johansen, an old friend of her father's. She asks about the P-51 and the Zeus Faber. He feigns igorance, only saying the ID number is wrong for a P-51. Later Johansen contacts her, and says he was an officer on the sub Zeus Faber that was sent to find the P-51 squadron. Scully later relays to Mulder what he said: the P-51s were an escort for a B-29 carrying an atomic bomb that never reached its target. Scully asserts they are now trying to retrieve the atomic bomb.
Mulder visits Kallenchuk Salvage Brokers to find a unhelpful woman named Jerry who says Kallenchuk is out of the country, while she secretly aims a gun at him. Mulder keeps surveillance on the place, and later sees armed French agents storm the office. Gerry flees in her car, and Mulder follows her to the airport, where she leaves on a flight to Hong Kong. Mulder follows her on to the flight, and Mrs Gautier follows Mulder on to the flight.
Skinner is confronted in a resteraunt by three men. The Gray-Haired Man says "we work for the intelligence community" and that Skinner should follow orders and keep quiet on the Missy murder case. They threaten his career otherwise.
Johansen tells Scully the story: The Faber found the sunken squadron just as a Japanese destroyer moved into the area. Capt Sanford ordered to stay; after a few days radiation burns appeared. Sanford continued to refuse to leave. One of the burned men tried to stage a mutiny but Sanford put him down; Johansen locked Sanford in with the sick and ordered them home, after a gunshot revealed their position. In the locked room, Sanford regards the sick men with the Black Oil running though his eyes. When they returned home, hardly any of the sick were still alive.
Mulder confronts Jerry in Hong Kong, demanding to know how much she charged the French for the P-51 squadron location and who is selling her the secrets. She says she's just a middle man, she came here to meet the buyer, a woman. Mulder handcuffs himself to her and has her take him to the Kallenchuk office, where he finds an armed Krychek waiting. Krychek throws Jerry out in the hall, with Mulder inside the office still handcuffed to her. The armed French agents arrive, and kill Jerry. Krychek flees out a window. Mulder unhooks himself and flees out the window. The French agents run into Mrs Gautier outside; her body flashes a bright white light. The men are now dying and horribly burned.
Skinner is at his resteraunt again. Luis Cardinal enters and harasses the waitress. When Skinner intervenes, Cardinal shoots Skinner in the gut, then spits on him and leaves. Scully is notifyed that Skinner was shot.
Krychek is about to board a flight to DC when Mulder captures him. Krychek says he didn't shoot his father and he doesn't know who did. Mulder wants the DAT Tape ("Anasazi") which Krychek has been using to sell secrets. Krychek says the tape was encrypted, that it's in a DC locker and he'll take Mulder to it if he lets him go. Mulder agrees and Krychek goes to the bathroom. Inside, Mrs Gautier attacks him. Outside, Krychek joins Mulder with the Black Oil running through his eyes.

Plot Points:

During WWII, a P-51 squadron escorted a B-29 carrying the 3rd atomic bomb to Japan. The planes were shot down, and the sub Zeus Faber was sent to investigate. Its captain became possessed by the Black Oil and most of the crew died of radiation. Now the French investigated the site, allowing the Black Oil to escape to the surface.
Enter the "Piper Maru" Black Oil: a sentient mobile oil that possesses humans and learns all their memories. It can release extreme radiation while leaving the host body unaffected. It constantly bleeds radiation which is leathal in large doses. It was discovered trapped at the ocean bottom where the Syndicate earlier salvaged a UFO. It is tracking down the conspirators who stole its UFO.
The Missy Scully murder investigation is over. Skinner protested, and got shot by Luis Cardinal in response.
Krychek has been selling US government secrets like the Black Oil's location through a middle man to foreign governments like the French. Now the French are gunning for him. Mulder thinks his information source is the encrypted DAT Tape he has.
Mulder captures Krychek and agrees to release for the DAT Tape. Krychek gets possessed by the Black Oil.

Analysis:

First off, the abilites and motivations of the Black Oil in this two parter are drastically different from its later appearances in "Tunguska"/"Terma", "Patient X"/"The Red and the Black", "The Movie", and "The Beginning". This will be discussed in detail for these episodes. Suffice to say the "Piper Maru" Black Oil is a single sentient alien which possesses humans, learns all their memories, can use the bodies to rad-flash as a weapon.
So this episode is 5 months after "Paper Clip", and the French have been searching the site for 2 months. This means that 3 months ago, Krychek and Jerry sold the location to the French. So within 3 months at the most Krychek was able to set up this business in Hong Kong with Jerry and get a buyer. Wow!
Apparantly the Black Oil's radioactive nature causes Gautier's audio and visual transmission to break up.
How did the Black Oil gets through Gautier's water-proof dive suit? This suggests that it either can move through sub-molecular openings (ie through anything) or that it somehow 'transmitted' itself. We see Black Oil getting through a Hazmat suit in "Tunguska", so perhaps it can just move through sub-molecular openings which nothing else can do. This suggests that the Black Oil's composition must be made of small, short-chain molecules at best, but how could something sentient exist in so simple a biology. Mulder suggests in "Apocrypha" that the oil is merely a 'medium' for its consciousness.
The Talapus and the Piper Maru were both based out of San Diego. Probably just a coincidense.
So the whole Piper Maru crew has horrible radiation burns. Either this was just from being in close proximity with a possessed human, or they discovered the truth about Gautier so he/it rad-flashed them to prevent a mutiny, and also to erase their memories of the revelation as the rad-flash causes delirium.
Scully asks if the radiation symptoms are acute or somatic. Acute means penetrating, and somatic roughly means wall of the body, ie non-penetrating radiation. So the Black Oil radiation flash only affects the near-surface of the body, rather than penetrating the body. This tracks with how the Piper Maru showed no radiation, because it 'somatic' then it would quickly bleed away. "Leukocytes and erythocytes" are blood cells, so a high count means that Black Oil possession doesn't affect your blood cell count. The doctor also says they suffer severe delirium. This is a very useful after effect; someone attacked by the Black Oil won't remember encountering the Black Oil!
The Black Oil has to absorb the memories of its hosts; how else could it speak English and successfully imitate its host. Notice that the possessed Gautier first ransacks the Piper Maru then his house, searching for where the French got their information from. We later learn the Black Oil is trying to return to its UFO, so its tracking down the people who stole it. So this means Gautier didn't know about Kallenchuk (actually the address), so maybe his wife was in charge of it (since the Kallenchuk letter is in his house), so Mrs Gautier must have been possessed because her memories would lead the Black Oil to Kallenchuk, the supplier of the UFO location. In any case Gautier is in on the French conspiracy since he refuses to talk to Mulder about Kallenchuk
Wow, isn't it an AMAZING COINCIDENSE that Scully's old family friend who she visits about the Zeus Faber just happened to be the XO of the Faber and have an encounter with the Black Oil alien?!
The timeline to this WWII flashback is very strange. In the last months of the war, the Japanese Navy was obilierated and the US Navy had the Japan islands surrounded. The atomic bombs were used as soon as they were ready (and they could acheive air superiority over Japan). So when does this flashback occur? An atomic bomb was being flown, but there was a Japanese destroyer around?! Of course we learn next episode that there was no 3rd atomic bomb involved! Then again, Johansen believes this cover story and he had to know about the course of the war, so I guess it is a writing inconsistancy after all!
Why exactly are these French agents gunning for Jerry and Krychek? Perhaps Jerry promised them a UFO at that location, and instead they picked up an alien that killed their crew, and they see that as a betrayal. Or perhaps they just want to kill her so she can't reveal these secrets to other nations. They do want to kill her, because they do in Hong Kong without even talking to her.
So who was Mrs Gautier follow to Hong Kong, Mulder or Jerry? Jerry later says she's here to meet the female buyer; in any case it's obvious this female buyer is the possessed Mrs Gautier. This could mean that Mrs Gautier was always the French contact with Jerry, and now she sets up a meet with Jerry, but then again Jerry is being chased by French agents so why would she agree to this? More likely, Mrs Gautier is contacting Jerry either for the first time or under a false name.
The Grey-Haired Man who threatens Skinner here will go on to become Cancer Man's silent right hand man in the Fourth Season and then he disapeers without explanation. And of course Cardinal is already shown to be a Cancer Man assassin, so Cancer Man ended the Missy investigation to cover the mistake of Krychek (thus his mistake) and then when Skinner tried to rock the boat he had Skinner shot to shut him up. Cancer Man continues to try and coverup his screwup in "Paper Clip" so the Syndicate doesn't learn. Or maybe Cancer Man is just getting his revenge against Skinner for when he screwed him over with the Albert Hosteen bluff in "Paper Clip".
So Sanford was possessed by the Black Oil. Once again the Black Oil gets through a water-proof diving apparatus to possess someone.
If Jerry came to Hong Kong to meet a female buyer, what was Krychek doing there? Presumably he lives in Hong Kong now, perhaps even in/near that Kallenchuk office and he just happened to be there. Remember, Mulder insisted on going there, Jerry didn't volunteer to take him there.
Krychek is very cruel towards Jerry. Is this just surprize and anger, or is their relationship always this cruel? If so, how did they get together in the first place?
Of course, we later learn Krychek is/was a Russian Syndicate mole into the Syndicate. So why didn't he just go back home to Russia and give the DAT Tape to his comrades? Apparantly Krychek truely is playing all sides, and is just out for himself.
Krychek is lying about not killing Mulder's Father. Obviously he's trying to survive Mulder's anger.
If the DAT Tape was encrypted and Krychek couldn't crack it, then where did he get his secrets from? Krychek was just a Cancer Man assassin, he shouldn't know about things like the ocean locations of UFO salvages. So maybe he somehow did crack the encryption of the DAT Tape. As we see in "Anasazi" the encryption was in Navajo, so maybe he grabbed a Navajo code talker... in Hong Kong? But maybe his Russian past comes into account here... maybe the whole time he worked under Cancer Man he was secretly gathering this type of information...
Wasn't it smart of Mulder to let Krychek in the bathroom himself! Why can't he just go in there with Krychek and watch him clean up and go to the bathroom? That wouldn't look suspicious, especially since the bathroom is empty. Plus, he doesn't even watch the freakin' door to see who else goes in there! What Krychek had a buddy nearby? Of course, if Mulder didn't act stupid then Krychek couldn't get possessed and he couldn't be stuck unknowingly with a leathally dangerous alien!

APOCRYPHA (part 2 of 2)

The Run Down:

Pearl Harbor 1953: three young government men from DC visit a dying survivor of the Zeus Faber. They record the conversation. He is covered with burns, and says he's the last one who knows what killed the crew, that it was a suicide mission. He was the one who revolted against Sanford, and when Johansen locked them in the crewmen attacked Sanford. The Black Oil ran out of his eyes, nose, and mouth into a vent. He says he saw the enemy that was killing them slowly. The lead man says "you called this thing 'the enemy'. You're saying it was an entity of some sort?". The survivor says they were sent to guard it, before it escaped back into the ocean, "back into who knows what". The lead man asks if this was what exposed the men to radiation. They go to leave, but the survivor insists that the thing is still out there, and that they have to make sure the truth gets out. He asks the lead man, Bill Mulder, if he can trust him. Cancer Man, the third government man, lights up and says "you can trust all of us".
Mulder and Krychek are driving to the DC locker. Mulder gets the locker key, but Krychek refuses to say where it is. They get forced off the road by another car and crash. Two men demand the DAT Tape from Krychek, who says he doesn't have it. One man punches Krychek in the stomach, but he isn't affected. Krychek rad-flashes the first man, and the second man runs to his aid. Mulder barely sees a second flash of light before passing out.
Scully checks on Skinner; the gun was found in a trash bin and prints were recovered. The investigating agents are slow to investigate or post guards on Skinner. Skinner is brought out of surgery. He tells Scully he's seen the shooter before. Cardinal's spit is found but it doesn't help. The DNA was pulled off hair, but they need the man to match it. Recent DC criminal records are searched for a match. Scully visits Mulder in the hospital to tell him about Skinner. The DNA of Skinner's shooter matches her sister's shooter. Skinner tells Scully the man was with Krychek in "Paper Clip". Scully petitons for the FBI to hunt for Krychek, who she believes can identify her sister's killer and the cause of the irradiated Piper Maru crew.
Cancer Man visits a hospital where his two agents are, horribly burned. The doctor says the burns are somatic "caused by close proximity radiation exposure" like the Piper Maru crew. Their days are numbered, and will soon get massive and malignant cancers. Cancer Man says he's seen this kind of thing before, and orders the (living) bodies destroyed.
Well-Manicured Man and the Syndicate Elders meet. First Elder says "we've received disturbing reports from our intelligence sources" about the irradiated crew of the Piper Maru, "its last given position was the site where we recovered the UFO". Well-Manicured Man asks where they could have learned that location. Second Elder says they don't know, "the French government has denied all involvement". First Elder says "it seems we have an information leak gentlemen". Well-Manicured Man asks "has our associate in Washinton looked into this?". First Elder says "apparantly he has responded to the situation in a way that I don't think any of us would have anticipated. I don't have all the details yet but I've asked him to here and explain it himself".
Mulder has the oil found on Gautier and his diving suit analyzed. Mrs Gautier was found in a Hong Kong airport bathroom, covered in the oil substance. It is 50 weight diesel oil, the kind used in WWII airplanes and submarines. "This oil is not only 50 years old, but its composition has been altered by exposure to radiation... I think it's a medium being used by some kind of alien creature that uses it to body jump". It's been waiting 50 years for another host to bring it up to the surface. He thinks its in Krychek now, and wonders what the Black Oil wants.
Cancer Man is relaxing at home when Krychek gives him the DAT Tape, asking "where is it?". Cardinal puts a gun on Krychek but Cancer Man hurriedly calls him off. Cancer Man says "I've been expecting you. I have what you want". The Black Oil runs in Krychek.
Cancer Man meets Well-Manicured Man and the Syndicate Elders. First Elder says "we've heard you acted on your own, and moved the salvaged UFO to another location". Cancer Man says "these new attempts to recover it have increased our need for security". Well-Manicured Man asks who else is looking for it, Cancer Man says "in the event, I moved it as a safeguard. I assure you it will be completely inaccessible now". Second Elder asks "why not bring it to Nevada, like the others?". Cancer Man says "leaks in security and heightened public interest have made the base in Nevada unviable". Well-Manicured Man says he was called here because of Skinner's shooting (Cancer Man says a random shooting for all he knows) and Cardinal's composite picture in the papers. Well-Manicured Man ids Cardinal as "one of yours". Cancer Man says if it's true he acted on his own. Second Elder says "this is a very serious exposure for us". Cancer Man says "I'll take care of it". Well-Manicured Man orders him to "get the shooter out of the country as quickly as possible, if the assistant director IDs him, our well placed operatives won't be able to stand in the way of arrest, compromising beyond repair the secrecy of our work, and the security as you so arrogantly assert of our project's future".
Mulder has the Lone Gunmen retrieve the DC locker (at an ice rink) for him; the envelope is empty but he gets an impression of a phone number off the envelope. Mulder calls and gets the 46th Street Syndicate office. Well-Manicured Man takes the phone. Mulder says he got the number from Krychek who killed his father. Well-Manicured Man recognizes him and asks for a meet. He then orders this number disconnected when the call is done.
Under Scully's pressure the investigating agents ID the shooter; "Luis Cardinal, native of Nicaragua, school of the America's alumni, career mercenary, apparantly impressed a lot of people with his markmanship during the Iran-Contra deal". Cardinal has entered the country illegally, but they have exhausted all avenues of investigation. He's probably out of the country already.
Mulder meets Well-Manicured Man in Central Park. Well-Manicured Man says he's after Krychek to kill him in revenge for his father, "what makes you think we haven't done that already?". Mulder asks what was pulled off the Pacific floor. Well-Manicured Man says "it was a UFO, a so-called foo fighter, downed by American fighter pilots in the 2nd World War. There were salvage attempts. A US sub was sent in 50 years ago, but there were complications. It's still a mystery. The cover story said it was a 3rd A Bomb bound to Japan, but the truth is, no one knows what killed that crew". Mulder says he knows, and offers that in return for Krychek. Well-Manicured Man asks why he didn't kill Krychek if he's meet him recently. Mulder answered "because he has the tape. The tape he's been selling those secrets off". Well-Manicured Man is surprised, and Mulder realizes he doesn't have Krychek either. Well-Manicured Man tells him "anyone can be gotten to, certainly you've no doubt of that". This spooks Mulder, and he leaves, calls Scully, and asks to check on Skinner.
Scully checks on Skinner and finds him gone; transfered to another hospital. She tracks down the ambulence and rides with Skinner. The ambulence stops; Cardinal arrives to kill Skinner but Scully surprizes him and Cardinal flees. Scully catches him and becomes enraged. Cardinal is afraid and offers Krychek's location for his life. Cardinal tells her Krychek is headed for an abandoned missile site in North Dakota. She calls Mulder and tells him, he thinks the salvaged UFO is there.
Mulder and Scully arrive at a decomissioned North Dakota missile site with 200 silos that should be filled with concrete. They find the silos are empty and being checking each one. They find some burned corpses of BlackOps troops, and Mulder knows Krychek is here. More BlackOps troops arrive and capture them. Mulder and Scully are taken outside, where they see Cancer Man. Mulder asserts Krychek is here and he led him here. Cancer Man says he doesn't owe him any answers. Mulder asserts the UFO is here and that's what Krychek's after. Cancer Man says Krychek disapeered 5 months ago. Scully says they say bodies with radiation burns, and Cancer Man says "you saw nothing!". Mulder and Scully are taken away into a van. Back in the base, Cancer Man has the bodies dragged away. Cancer Man glances in Silo 1013 before leaving. Inside Silo 1013, Krychek is on top of a large triangular UFO. The Black Oil is running out of his eyes, nose, and mouth, into a spiralling grid pattern. The Black Oil disapeers into the center of the pattern.
Skinner returns to work and tells Mulder he was only hoping to bring a criminal to justice. Cardinal died in his cell of a 'suicide'.
Back in Silo 1013, Krychek is back to his normal self, trapped inside with a motionless UFO. He bangs on the door, begging desperately to be let out.

Plot Points:

In 1953, Bill Mulder and Cancer Man were part of a Group that investigated the "Piper Maru" Black Oil, and learned it was a sentient entity that leaked radiation. Bill Mulder was already doubting keeping it a secret.
Survivors of a "Piper Maru" Black Oil radiation attack will get massive and malignant cancers until they die.
First Elder alerts Well-Manicured Man and the Syndicate to an information leak and the Piper Maru situation, as well as Cancer Man's unantipicated response.
The oil of the "Piper Maru" Black Oil is 50 year old 50 weight diesel oil from WWII planes and subs. Mulder asserts that an entity is using it as a medium to body jump and possess a host.
A "Piper Maru" Black Oil possessed Krychek returns the DAT Tape to Cancer Man in return for being taken to his UFO.
Cancer Man moved the Talapus UFO without permission because of new attempts to recover it.
Most Syndicate salvaged UFOs are taken to a Nevada base, but Cancer Man thinks its useless now because of security leaks and heightened public interest.
Well-Manicured Man threatens Cancer Man about the Skinner shooting debacle and orders him to remove Cardinal from the country.
Well-Manicured Man thinks that Skinner IDing Cardinal would cause the arrest of several "well placed operatives" and would comprimise "the security of our Project's future".
Mulder gets the 46th Street Syndicate Office phone number and calls Well-Manicured Man. They meet and the number is changed.
Well-Manicured Man learns from Mulder that Krychek is alive and has the DAT Tape, and is the Syndicate's information leak.
Cancer Man returns the "Piper Maru" Black Oil to its UFO in an abandoned missile silo, leaving Krychek trapped inside as well.
The FBI identifies Cardinal, a Nicaragua mercenary from the School of the Americas. Scully catches him trying to kill Skinner again, and Cardinal commits 'suicide' in prison.

Analysis:

So in 1953 there existed a Group who investigated alien encounters, including Bill Mulder and Cancer Man. Popular opinion is that their third compatriot is Deep Throat, but I think it's First Elder. In any case, this is apparantly where they first encounter the Black Oil; Bill certainly doesn't recognize the Black Oil when the survivor describes it.
A possessed Krychek shrugs off a gun to the gut. Presumably the Black Oil can just turn off or ignore pain receptors.
These investigating agents on Skinner's shooting seemed to be in with the Syndicate; they practically refuse to actually investigate the case and they fail to post guards on Skinner, plus later these guards that Scully insisted on disapeer and Skinner is taken. Does Scully ever do anything about these two?
Cancer Man says he's seen Black Oil radiation burn victims before. This may only refer to the survivor at the episode beginning, but what if there have been several outbreaks like this? Then again, that would even further confuse the issue of the Black Oil.
Time for some Black Oil brain-twisters. The Syndicate knows that the Black Oil has been on the Pacific floor for 50 years, so presumably they are keeping it trapped there. Then they steal its UFO in "Nisei". Seems like they're trying to keep it trapped on planet under the ocean. So from this two-parter we may safely assume that the Black Oil is one of the evil aliens that the Syndicate hates. First Elder is not happy about Cancer Man helping the alien back to its UFO (which makes sense because they are the ones that stole it). Yet ultimately we learn that the Black Oil IS the Colonists, with whom the Syndicate collaborates with. So what's up with this Black Oil? Could it be some kind of rebel Black Oil, related to the Faceless Rebels in "Patient X"/"The Red and the Black" and "Two Fathers"/"One Son"? Yet we apparantly learn that Pilots do not carry Black Oil, and the Rebel Pilots seal their faces so they can't get infected by Black Oil so presumably they don't already have some. This suggests that there are no 'rebel' Black Oils, that they are a group conscious. I think my brain is going to explode...
Another brain twister: when the Black Oil possesses a host, it gestates a Mutated Grey in "The Movie" and "The Beginning". Yet here a possessed host isn't affected! And possessed hosts in "Tunguska" just go comatose! The only possible explanation is that the "Piper Maru" Black Oil doesn't allow the gestation process to begin (if he's a loyal Colonist then its to keep the secret, if its a rebel I have no idea). And as for the "Tunguska" Black Oil, we'll deal with that then.
In the first Syndicate meet, First Elder seems to play the role of intelligence officer, though he's pretty much just ratting out on Cancer Man because he hates him.
We see that the Syndicate owes no alleigance to the French government.
First Elder announces they have an information leak. Well-Manicured Man later learns from Mulder this leak is Krychek and the DAT Tape. Yet we never see anything more of Well-Manicured Man. If he remains silent about what he learns, First Elder will continue to investigate this security leak. If he does tell them, then won't the Elders (especially First Elder) demand Cancer Man's head for lying to them about Krychek's death and the destruction of the DAT Tape?! Yet we never hear anything more about this, and the next Well-Manicured Man meets Cancer Man (in "Tunguska") he's almost friendly with him! And, in First Elder's next appearance about a third of a year from now in "Herrenvolk", he's going on about an information leak which turns out to be X. Is this a second information leak he discovers, or he still searching for this one?
First Elder says Cancer Man has responded in a way they don't like. But at this point all he's done is send two assassins after Krychek and Mulder, and then kill them after getting toasted. Why is this wrong in their eyes? Since they don't know about Krychek yet, as far as they know Cancer Man sent some assassins after Mulder who has been investigating this radiation thing, and the assassins came back irradiated. This most likely means the Syndicate now knows the "Piper Maru" Black Oil is involved.
How could the possessed Krychek get in Cancer Man's apartment without making any noise? Maybe Cancer Man left his door unlocked, waiting for the Black Oil to contact him. Perhaps the unliked action that Cancer Man took was to somehow contact the Black Oil (ie possessed Krychek) and offer a deal: DAT Tape for UFO. Of course, First Elder can't know about the DAT Tape or Cancer Man'd be in trouble. So First Elder must have learned that Cancer Man contacted the Black Oil and offered return to the UFO. Again this makes the Syndicate out to be the enemies of the Black Oil. Maybe it is some kind of rebel Black Oil...
If Cancer Man left the door unlocked, it makes sense that he'd have an assassin in the next apartment for security just in case it was an enraged Mulder like in "One Breath".
Hopefully Cancer Man promptly destroyed the DAT Tape after receiving it, as he said he did to the Syndicate in "Paper Clip".
Cancer Man mentions new attempts to recover the salvaged UFO prompting him to move it. What does this mean? Are other alien UFOs searching for it or something?! More likely it's just enemy nations like the French, the Japanese, and/or the Russians.
So most salvaged UFOs are kept in a Nevada base. This is NOT Area 51, but that tracks because in "Dreamland II" we learn that Area 51 is military run and they have no idea about the existance of aliens.
Of course, the very concept of salvaged UFOs means that there are aliens seperate from the Colonists, as has long been shown. But how exactly are they shooting these things down in the first place? Perhaps the Colonists keep a small space fleet near Earth and shoot down any interlopers trying to mess with their next target. Then again, we repeatedly see different aliens freely visiting Earth so this is unlikely.
The Syndicate is able to ID Cardinal as a Cancer Man assassin. This means they must have a list somewhere of Cancer Man's assassins.
This episode seems to prove once and for all that Cancer Man's role in the Syndicate is to run the assassins and coverup crews. He operates out of Washington, and also seems in charge of controlling the FBI. Then again, according to "One Son" he's in charge of the entire abduction/Hybridization program, which seems waaaay too much for him plus its a tad out of the blue.
Well-Manicured Man says that Skinner IDing Cardinal would lead to several well-placed operatives being exposed and The Project's security being threatened. Yet Cardinal is proven to be Skinner's shooter, and nothing happens!
It makes perfect sense that Krychek had the 46th Street Office number on the DAT Tape envelope. At the end of "Paper Clip" Krychek calls that office with the DAT Tape in his possession.
Well-Manicured Man, as in "Paper Clip", tells Mulder a mix of the truth and then lies. He admits that a UFO was shot down by WWII fighters (how could those primative fighters shoot down a UFO for god's sake, but then again that's the only explanation for the UFO crashing) and about the 3rd atomic bomb lie but then lies saying no one knows what caused it. Like a loyal Syndicate man he is above all keeping the secret of collaboration with the Colonists, by here lying feigning ignorance about the Black Oil when in fact it is the very thing they are working for!
Well-Manicured Man tells Mulder anyone can be gotten to, and suddenly Mulder gets the inspiration that another attempt is about to be made on Skinner. This seems a like an amazing leap of logic for Mulder, and a conveinent one as well!
For being such a wonderful mercenary, Cardinal is a woefully inept assassin. First, he shoots Missy instead of Scully in "The Blessing Way". Then, in "Piper Maru" he shoots Skinner but fails to kill him. Here, he once again botches murdering Skinner and gets captured by Scully of all people! One wonders why Cancer Man would continue to use this guy after screwing up with Missy. Cancer Man seemed to blame Krychek for that for some reason. Then again, all of Cancer Man's assassins seem to woefully inept.
So Cardinal knows where Cancer Man is taking Krychek. That makes sense, he was with the two of them when they made their little plan. But he doesn't know which abandoned North Dakota missile base (there must be more than one!).
It's an amazing peice of investigative work that Mulder and Scully manage to figure out which abandoned North Dakota missile base to go to in such a limited time!
Why did the possessed Krychek torch those BlackOps troops? Was is just in spite? So apparantly Krychek went alone into the base save these few troops who showed him which silo (ie Cancer Man wasn't there), and when they showed him he torched them because he was in a bad mood.
These BlackOps troops wear uniforms identical to the Police Swat Team's uniforms seen in the next episode "Pusher". This is almost definitely a budget constraint problem rather than an indication that the most top secret troops in the world are actually Police.
Why does Cancer Man return with BlackOps to the base? Presumably he's been keeping tabs on Mulder, and learned he found the base so he showed up to remove him. Plus Cancer Man also wanted to sneek a peak for himself to make sure Krychek was in with the UFO.
So Mulder and Scully take a van ride with some BlackOps troops even though their car is right there. Where were they taken? And what was it like in that van? Was Mulder screaming about seeing the truth the whole time?
So the Black Oil just wanted to go back inside its UFO. Apparantly after that it seems content to just sit there in the silo. Is it going to 'hibernate' there indefinitely? Could this be a Black Oil awaiting its usefulness come Colonization time, like the Black Oil deposits in the Texas Caves in The Movie?
So Krychek and the UFO stayed in that same silo. If Mulder had a single brain cell he would RETURN TO THE BASE, and if he did he would have found Krychek and the UFO, and he would Krychek and his proof of aliens. But of course, he never returns! Maybe he just assumed that Cancer Man would have removed all the evidense, but he should really follow through!
And really, how long will Krychek be trapped there? The human body can only survive about three days without any water at all, so unless somebody comes by to release Krychek, he'll die. Of course we know he escapes the silo because he returns alive in "Tunguska", but we never hear of the "Piper Maru" Black Oil or its UFO again.
Here's a theory: after a few hours of resting, the Black Oil UFO takes off. Krychek jumps on top, and rides it up to the surface, then he jumps off it to the ground while it flies away. He then joins up with that milita in "Tunguska".

JOSE CHUNG'S FROM OUTER SPACE

The Run Down:

On a Washington county there is a mysterious power failure. Rocky is called out to investigate. Harold and Chrissy are driving in a car when the car looses power. A bright light appears, and a UFO lowers down to hover near the surface. Two people approach them, dressed up like classic middle-sized Grey aliens. Harold and Chrissy pass out, which seems to surprize the two 'aliens'. They are dragging the two towards their UFO when another UFO appears, targeting them with a red light. A giant creature jumps down from its spaceship and approaches the two 'aliens' yelling at them. The two 'aliens' have no idea what it is.
Famous author Jose Chung wants to write about alien abductions. Mulder refuses to speak with him, but Scully is a fan and agrees. The book was Chung's publisher's idea. Chung has interviewed the involved parties of the Washington case for three months, and has learned that everybody has a subjective version of the truth.
Scully narrates... the next morning the car was found by the road. Chrissy was inside, suffering from physical abuse. Her clothes were on backwards and inside out, and she had no memory of the previous night. That night while sleeping Chrissy gets a nose bleed. Harold called to Chrissy from outside saying he did everything could and was surprized she didn't remember. Harold was arrested. He said they were abducted by aliens, and a lie detector proved it. But when Mulder and Scully arrive, Harold says he must have raped her. Mulder questions Chrissy and she has "post-abduction syndrome"; trouble sleeping, muscle pains, vision problems, nose bleeds, looking at an object and seeing an alien's face.
Jose Chung says the CIA conducted MK-Ultra mind control experiments in the '50s but had no idea how hypnosis works. Scully says it's still unknown today, and she thinks it doesn't enhance memory but worsens it because the suggestive state of hypnosis.
Mulder has Chrissy undergo regression hypnosis; she remembers being in the UFO, attached to a verticle slab of metal with white running details on it. There are Little Greys standing around her (in an identical position to the people in the hypnosis room!) and a dazed Harold is attached to a similar horizontal slab. They are both naked, but are covered with metal impliments. The aliens are arguing amonst themselves, but she can hear the leader in her head; his mouth doesn't move. The leader tells her this is for the good of her planet, but she feels he's stealing her memories. Mulder says its a classic abduction scenario.
Harold narrates... he is with an unconscious Chrissy in a small cage of crude metal bars. There are many such cages around with electrified bars, and they can hear distant screams. In a nearby cell is Jack, one of 'aliens' who just smokes a cigarette. Harold promises to protect Chrissy, but when the giant creature arrives and the cage cieling opens, Harold cowers and the creature takes Chrissy. The whole time Jack is just rocking back and forth, saying in English with his mouth "this is not happening!". Harold is then taken too, but he saw nothing because he was cowering in fear the whole time. Harold then remembers flying through the air and hitting the ground. He then ran immeadiately to Chrissy's to check on her. He had sex with Chrissy earlier.
Rocky calls the police to say he witnessed the alien abduction. Mulder and Scully visit him. He has written his experience down, but fears for his life because the night before he was visited. He was writing in his garage, when the door suddenly opened by itself. A black seden pulled in with unnatural speed. A Man in Black got out of the car and told Rocky that Venus is often misidentified as a UFO, and that Venus was at peak brightness last night. Rocky says he was a trance because he wasn't angry at the intrusion. He can't remember their faces, only that they were dressed in all black. Mulder says that since the '50s people who have close encounters later meet the men in black. [Jose Chung says that men in black garments have appeared throughout history in many different cultures. Celtic legends have trickster men in black and any who encounter them become enchanted.] The Man in Black says "your scientists have yet to discover how neural networks create self-consciousness" or how the brain creates a 3D image from 2D images. He says "your scientific illiteracy makes me shudder" and if he tells anyone about what he saw, he's a dead man. The Men in Black drive off. Rocky hands them his abduction manuscript and tells them he's going into hiding.
Mulder reads Rocky's transcript: he drove up to Harold's stalled car, and his van stalled. He saw the giant creature swinging his arms at the two 'aliens' who ducked under the blows. The giant creature then walks over to Rocky's van where he is cowering. 'Lord Kinboate' says "be thou not afraid! No harm will come unto thee. Your efforts are needed for the survival of all Earthlings. Come! I shall showeth thee!". Rocky then took a ride aboard his "hover vessal" to the inner earth, the Earth's molten core, the domain of Lord Kinboate. [Chung received a copy of the manuscript from his publishers. In the 'inner earth' there was a sexual orgy of reincarnated souls! Rocky also describes lava men.]
Mulder thinks that Rocky's story supports Harold's story, so has Chrissy re-hypnotized. She remembers the giant creature beating her while she cowered, then she was flying through the air. She then remembers men in Air Force uniforms lifting her off the ground. She then remembers being in a office, surrounded by suited and uniformed men who stand in identical positions to the aliens and to the people in the hypnosis room. She is being hypnotized by a doctor while the other men argue. Air Force Man says "ask her if this third alien had a Russian accent". CIA Man says "this is way beyond their capabilites. This is way beyond our capabilites". CIA Man 2 says "ask her if she knows where the grey alien's saucer went to". CIA Man says "how is she going to know that?". Air Force Man says "have we located any of the others?". CIA Man 2 says "we're combing the area but this weather makes it tough". CIA Man says to the doctor "rinse her out, and get her the regular abduction rigmarole". The doctor then tells her it's for the good of the country, but he's stealing her memories.
Blaine the geek was UFO hunting in the woods because of some recent sightings in the area. He trips over the body of an 'alien' and calls the police. Mulder and Scully arrive with the police; Blaine latter tells Chung they were Men in Black and threatened him. Blaine later tries to break in on Scully's 'alien' autopsy and Mulder lets him record it with a camcorder. This footage is later used for an fake alien autopsy video. Scully discovers the 'alien' is actually a dead human in a rubber alien suit. Scully checks the military database and finds it is Air Force Major Vallee. Right after she checks Air Force Man (from Chrissy's abduction) arrives to collect the two AWOL pilots. Mulder lies and get the second pilot's name: Lieutenant Jack Shaffer. Air Force Man doesn't get Vallee's body and leaves.
The two Men in Black (from Rocky's story) arrive at Blaine's and take his alien autopsy videotape then knock him out. Later Mulder and Scully arrive (from Blaine's POV) dressed in black and threaten him again if he talks about it.
Mulder finds a mutilated, dazed and naked Jack Shaffer walking down the highway. Jack tells him about military UFOs in a diner: "...used to project the image of the Virgin Mary over the French trenches in WWI. The enemy's always willing to fire upon an invading force... but on a holy miracle? The enemy sees an American recon plane, they start shooting. They see a flying saucer from another galaxy... they hesitate. You know what happens to most people after seeing a UFO? [Missing Time Mulder answers] Any number of 'soft option kills' will do, nerve gas, low frequency infrasound beams, hell with high-powered microwaves, you can not only cut enemy communications, you can cook internal organs. [Mulder asks about the abductions] Don't know as much about them. I'm just the pilot. You ever flown a flying saucer? Afterwards, sex seems trite. [Mulder asks what is done with the abductees] Take them back to the base. Let the doctors work on them. Nothing physical, they just mess with their minds. At the base, I seen people go into an ordinary room with an ordinary bunch of doctors, and come out absolutely positive they were probed by aliens". Mulder asks what abducted him if alien abductions are just a covert military operation. Jack says he's positive he, his co-pilot, and the two kids were abducted but he's not sure if anything is real, even right. Air Force Man arrives with some soliders, Jack says he's a dead man. Mulder asks about the third alien as Jack is taken away. Jack says "Who? Lord Kinboate?". The cook at the diner later told Chung about Mulder quizzing him about aliens while eating an entire sweet potato pie but didn't mention Jack at all.
Mulder goes to Scully's hotel room to find the door unlocked. The two Men in Black are there, searching Scully's room. The Man in Black says Scully went to get some ice, and Scully calmly returns with a bucket of ice. She says these men have something very important to tell Mulder. The Man in Black says "some alien encounters are hoaxes perpetrated by your government to manipulate the public. Some of these hoaxes are intentionally revealed to manipulate the truth-seekers who become discredited if they disclose the deliberately absurb deception". Mulder says that Men in Black dress and act strangely for the same reason, so no one would believe someone if they talked about encountering them. The Man in Black says "I find absolutely no reason why anyone would think you crazy if you described this meeting of ours". The Second Man in Black, who is identical to game show host Alex Trebeck, tells Mulder he's feeling very sleepy. Scully has no memory of this encounter and woke up the next morning to find Mulder sleeping on the couch in her hotel room. Mulder remembers though.
Mulder and Scully are called in. A military plane crashed; it was a top secret experimental plane which was the cause of all these alledged UFO sightings. Soldiers carry away the bodies of Jack Shaffer and Robert Vallee.
Mulder meets Jose Chung and tells him not to write the book. He will ridicule the truth seekers by trying to describe the events that "deal with alternative realities that we're yet to comprehend". Also, his publishing company is owned by a military supplier, so Mulder suspects a covert agenda from the military-industrial-entertainment complex for his book. Chung says he will write the book.

Plot Points:

In America, alledged alien abductions are actually Air Force pilots dressed in rubber Little Grey suits flying military UFOs. The people are abducted then taken back to the base where they hypnotized and given false memories of an unbelievable alien encounter. They are all fed the same story so that no one believes anyone who comes forward.
Mulder describes typical post-abduction syndrome: trouble sleeping, muscle pains, vision problems, nose bleeds, looking at an object and seeing an alien's face. The person's clothes are inside out and backwards when they are found.
A typical military abduction went horribly wrong when a large alien creature arrived in a UFO and abducted the Air Force pilots and the abducted teenagers. They beaten and mutilated, and one Air Force was killed. They were then returned. The Air Force and CIA suspected the Russians but the alien was too advanced. A pair of Men in Black threaten witnesses, one of who looks like Alex Trebeck.
Men in Black have been threatening alien witnesses since the 1950s, but strange men in black have appeared throughout history in various cultures. They are sometimes tricksters who enchant those they encounter.
Mulder meets one of the UFO pilots who tells him the UFOs are made to look alien so the enemy won't shoot at them. The UFO is then used for 'soft option' kills using nerve gas, sound weapons, and high-powered microwave emissions.
Mulder meets a Man in Black who tells him only some alien abductions are government hoaxes to discredit truth seekers.
The military-industrial-entertainment complex secretly publishes books to discredit truth seekers.

Analysis:

This was an extremely confusing and suspect episode due to the many different POV stories which pretty much all conflict with each other. With one glaring exception, on closer inspection most of them match.
Here is the truth: Harold and Chrissy were approached by Jack and Vallee, who had come to abduct them, take them back to the base in their UFO where they would get false abduction memories. But before they could leave another UFO arrived, carrying a real alien. This alien saw the two 'Grey aliens' as its enemy and abducted them all. Rocky witnessed this event from a distance, and heard the alien's name Lord Kinboate in some kind of telepathic broadcast which Jack also heard. The alien left with Harold, Chrissy, Jack, and Vallee in his UFO. He took them somewhere large but primative looking where he tourtured Jack and Vallee, killing Vallee. Harold and Chrissy were beaten some. He then returned Harold, Chrissy, Jack, and Vallee's body to different places. Chrissy was found by the Air Force, and given the false abduction memory by the hypotist. Two Men in Black, who were most likely Syndicate-affiliated, came forward to wierd out and threaten Rocky. Harold retained his memory of the real alien encounter, drawing in Mulder. Rocky came forward with a hallucinated truth. Blaine discovered Vallee's body, which was then recovered by the Air Force. The Men in Black threaten Blaine. Mulder found Jack naked and dazed. The Air Force grabbed Jack, killed him, then staged an airplane crash to explain away the UFO sightings and death of Vallee and Jack. The Men in Black then visited Scully and hypnotized her to forget the encounter, however Mulder found them there. The Men in Black used hypnosis to confuse Mulder, but he remembered the encounter. To further coverup the issue and to continue the discrediting of truth seekers, they commissioned Jose Chung to write a book about the event that would make it appear totally ludicrous and unbelievable. The book gets written.
Military/Syndicate UFOs cause power failure in close proximity.
The Air Force UFO was traditional saucer shaped and Lord Kinboate's UFO was the triangular Syndicate/Colonist model. Of course, this doesn't make any sense it should be the other way around. But if this is right, then it means the Syndicate also has saucer shaped UFO models (we see a similar saucer UFO in "Duane Barry" which logically would be a Syndicate UFO) and that Lord Kinboate may be in some way related to the Colonists. My theory: he's an enemy of the Colonists (that's why he attacks humans dressed up as Greys), maybe a people that they once tried to conquer but failed and he's come to bust some Colonist ass. Then again, Lord Kiboate's UFO looked more squat than the Colonist model.
Do Jack and Vallee use any kind of weapon to make Harold and Chrissy pass out, or did they just feint? For them to feint at the same time makes it seem like a weapon; maybe the sound weapon Jack later speaks of. And if they just happened to feint, then how do the Air Force pilots drag them on to their UFO if they're awake and kicking? Yeah, definetly some kind of weapon.
Lord Kinboate looks much too large to fit in his UFO! Perhaps that red light is some kind of shrinking/enlargening ray that shrinks Lord Kinboate for travel then enlargens him for exit.
Since the teaser is not narrated by anyone, it should be considered the truth. However, with the exception of the Chung-Scully scenes, the rest of the episode is narrated and thus suspect.
So who turned Chrissy's clothes inside out and backwards? Not Lord Kinboate, the Air Force after they recovered her and stole her memories of the encounter.
Chrissy gets a nose bleed; throughout the series this is associated with an abductee who has an Implant, usually in the neck. But its doubtful that after the rush to steal Chrissy's memories and return her, the Air Force had time to Implant her. In fact, maybe nose bleeds are just from close proximity with the UFOs. This entire case seems unconnected with the abduction/Hybrid program. Perhaps the UFOs are used for two seperate operations: these type of short abductions to discredit alien abductees, and then the real ones where women (and sometimes men as we learn in "Field Trip") are taken for a month, and forced to bear a Hybrid child.
So the positions of the observors of Chrissy's regression hypnosis mimick the positions of the observers in Chrissy's false and real abduction memories. This must be an altered rememberance rather than a coincidense, but the other memories are trustworthy.
The prison that Lord Kinboate takes the four humans to doesn't look very alien, in fact it looks very primative. Does that mean that Lord Kinboate wasn't really an alien? The Air Force agents don't think the Russians capable of such a thing, so it seems unlikely. Yes, Lord Kinboate was a real alien!
Why did Lord Kinboate mutliate and beat his human prisoners? Perhaps he tried to interrogate one of his 'Grey' prisoners, and was shocked to learn it was actually a frail human (maybe he killed Vallee accidently, thinking he was made of sterner stuff).
And why do Harold and Chrissy feel flying through the air then hitting the ground? Does Lord Kinboate kick them off his ship while its still hovering a few feet off the ground?
And why did Lord Kinboate keep Harold for a day when he kept Chrissy for only that night? And why did Jack only appear two/three days after the abduction. Perhaps Jack was returned in the middle of the forest, and it took him this long to get to a road where Mulder finds him. Still though, Harold says he went right to Chrissy's when he was returned. So why was he kept an extra 12 hours?
Obviously Rocky's story was bull aside from first pulling up to see Lord Kinboate and the two 'Greys'. In fact, it even seems doubtful that Lord Kinboate would swipe his arms at them when they're about five feet below his arms.
Rocky's perception of the Men in Black could have been altered by Alex Trebeck's hypnosis, so that he remembers their car driving abnormally fast. Or, the Men in Black could just be Syndicate members and use alien technology in their cars. Plus, this hypnosis could be why he can't remember their faces or why he remembers being caught in a trance.
Mulder says that since the 1950s people have met Men in Black. Well, since the Syndicate formed in the late 1940s it seems very likely that these Men in Black are in fact Syndicate agents covering alien knowledge. But the fact that men in black garments are recorded throughout history suggests otherwise. Either its just a coincidense (one purposefully made by the Syndicate?) or Men in Black are actually Pilots sent by the Colonists to scope out how humanity is progressing, waiting for it to be ready for Colonization.
During Chrissy's real encounter with the Air Force, one of them asks if they've found any of the others, and another replies that the weather is making the search tough. Obviously this shows that the Air Force is searching for all four humans involved, but have only managed to find Chrissy because of the bad weather.
The Men in Black steal Blaine's videotape of the 'alien' autopsy and it later appears as a cheesy show on TV. Did Blaine have a copy that he sold, or did the Men in Black actually sell it to TV to further discredit the truth seekers. If they did, it makes the Men in Black seem to be human Syndicate members very much and not Pilots.
So Scully checks Vallee's face or something with a military database. This sets off red flags, alerting Air Force Man so he rushes over the hospital to collect his 'AWOL' pilot(s).
Air Force Man leaves the hospital without Vallee's body, yet later it appears at the crash site. So how did he get it? Did he just wait for Mulder and Scully to leave the hospital before stealing it?
The fact that both Rocky, Blaine, and Mulder all seperately see the same Men in Black makes them real. Though since only Mulder sees Alex Trebeck (though Blaine appears to see him too) that means the Trebeck face was just a hypnotic suggestion. Or less likely, the Men in Black are Pilots and they morph their faces to look like famous people (but this doesn't track with the historical accounts saying that no one remembers their faces).
Conspiracies are afoot... here we see professional wressler Jesse Ventura is a Men in Black. Just three years later... he's elected Governor of Minnesota!
Jack tells Mulder that these UFOs were made as spy planes the enemy wouldn't shoot at. While that may be true to some extent, we never see Syndicate UFOs do much aside from test flights and abducting poor schmoes. Plus, why would the Syndicate care about what the Russians are up to? They're fighting aliens for god's sake! Then again, we see in "Dreamland II" that the military are given the UFOs and they pretty much do what they want with them, so maybe its just the military alone doing this.
Jack also seems to speak of the UFOs as a way to sneak into enemy terrortory then attack with nerve gas, sound weapons, and microwave weapons. Again, there doesn't seem to be much need for this.
Jack says he doesn't know as much about abductions as he does about the military applications because he's just the pilot. Does this that his co-pilot (who is of higher rank than him!) is in charge of the people they grab, while he just flies the ship?
Obviously Jack has never participated in abducting women for the Hybrid pregnancy operation, or he's lying to Mulder about it.
How can Jack know Lord Kinboate's name, a crazy sounding name that Rocky gave him? My theory is Lord Kinboate send out some kind of telepathic signal announcing his name; Jack and Rocky heard it.
Obviously the Men in Black hypnotized Scully so they could search her room for any damning evidense.
Notice the Man in Black says some alien encounters are government hoaxes; the rest are human-run abductions for the Hybrid program and there are a few occaisonal true alien abductions from non-Colonist aliens.
Scully is hypnotized to forget her encounter but Mulder retains his (probably altered) memory. Why bother leaving him with the knowledge? Probably just to further discredit him even with his partner if he starts talking about Men in Black.
It's interesting that the conspirators will go to all the trouble of publishing novels just to discredit the alien truth.
Mulder says this case deals with alternate realities. What does this mean? Does he mean altered memories? That's not alternate realities, that's brainwashing!

AVATAR

The Run Down:

Skinner stalls agreeing to a divorce; that night he encounters a woman, Carina Sayles, at a hotel bar and they go to her room to have sex. He has a vision of an old woman instead of Sayles and awakens to find Sayles dead, her neck broken.
Skinner is arrested. He refuses to take a lie detector test and refuses Mulder's help. Sayles turns out to be a classy prostitute. Scully examines the body; she died of a sudden attack without a struggle, and Sayles has a strange phosphoresence around her mouth and nose. Mulder and Scully meet Sayles' pimp Lorraine Kelleher, who runs prostitutes for powerful government men. Sayles called her last night with Skinner's credit card. Mulder is adamant to help Skinner after all the help he's given him, Scully doubts his innocence.
Skinner is released, Mulder tells him Sayles was a prostitute which Skinner didn't know. Skinner sees the old woman again, but it is actually Sharon Skinner his wife. Sharon tells Mulder and Scully they've been seperated for 8 months because Skinner ignored her. She says Mulder is the only person he ever mentioned from work, it sounded like he respected him. Mulder tells Sharon he's innocent.
Mulder and Scully find an OPR Agent searching Skinner's desk. The OPR will interview them to see if Skinner should be fired. Skinner has REM sleep behavior disorder, and has been treated for it the past 3 months at Bethesda Sleep Disorder Center. Skinner has nightmares about an old woman; Mulder traces it to the Succubus, an old legend of a spirit that visits men in the night for sex or to protect them jelously from other women. Sometimes the victim had a phorphoresent glow afterwards. Scully tells Mulder about Sayles' glow but when they check the body again it's gone. The analysis of the sample she took was salavia and unidentifyable substances.
Skinner wakes from his sleep to see the old woman screaming. He then gets arrested; Sharon was forced off the road by a car and is near death. Mulder meets Skinner in a police interrogation room; unbeknownst to them they are observed by Cancer Man. Mulder asks about the old woman, Skinner says she began to appear again a few months ago. He first saw her in Vietnam when his squad was ambushed and he was near death; she saved him from death. Mulder asserts she protected him then, and she's protecting him now.
Skinner's car seems to be the one that forced Sharon off the road. Mulder takes the exploded airbag to Pendrell; he can reconstruct the face of the driver from the impression in the airbag. Scully and Skinner meet the OPR Board; they accuse both of them of being enchanted by Mulder to believe his crazy theories. Skinner signs off on anything Mulder wants, and Scully seems to be trumping up unidentifyable evidense (the glow) to protect Skinner. Skinner is suspended. Mulder asserts that "they" found Skinner's weakness and exploited it to weaken him and the X-Files. He thinks that a second assassination attempt on Skinner would be too obvious even for them, and he is better discredited than dead. Pendrell has gotten the composite face of the man who stole Skinner's car and tried to kill Sharon, Mulder asserts he is a pawn and he also hired Sayles.
Kelleher has committed 'suicide', jumping off from her high apartment. Mulder and Scully arrive and find Judy Fairly, another prostitute, who agrees to help them. She says "they" would set up some kind of surveillance device in the room to blackmail the client. She identifies the composite as the man who hired Carina, Mulder convinces her to call him and ask for a meet for money. She calls Air Bag Man, who gives the phone to Grey-Haired Man. Grey-Haired Man agrees to the meet, but he is watching Fairly sitting with Mulder and Scully. Skinner visits his unconscious wife, and tells her he grew cold because in order to follow the orders of his superiors who spread violence and lies he had to turn a part of himself off, but coming home to her was the only light in his life. Sharon's pulse suddenly increases setting off alarms. Skinner sees the old woman briefly and Sharon awakens to tell Skinner something.
Scully is waiting with Fairly in a hotel room while Mulder and police guard the entrance. They do not see Air Bag Man sneek up to the hotel room, where he enters quietly and knocks out Scully. He is about to kill Farily when Skinner arrives and shoots him dead. Air Bag Man's face and fingerprints do not appear in any database. Grey-Haired Man's phone line has been disconnected and there is no record of an account. Skinner thanks Mulder and Scully for their help but refuses to say how he knew to be at the hotel room.

Plot Points:

When Skinner had a near-death experience in Vietnam, he was saved by a Succubus who protects him still.
Skinner is married to Sharon Skinner, but they've been seperated for months and she wants a divorce.
Cancer Man orchestrates a scheme to frame Skinner for murder, including that of his wife using his Succubus problem. It fails thanks to the Succubus and Sharon survives her attack.
The OPR Board thinks that Skinner and Scully have become 'enchanted' by Mulder.

Analysis:

It's funny that we never hear a single mention of Skinner's wife in the first SIX seasons of the show aside from this one episode!
So Grey-Haired Man hired Sayles to screw Skinner, then set it up so Skinner wouldn't know she was a hooker. Then while they were sleeping Air Bag Man slipped in and broke Sayles' neck. The Succubus sensed the attack and tried to warn Skinner in his sleep, but failed. Then the Succubus again tries to warn Skinner about the plot to kill Sharon by appearing as Sharon. When Air Bag Man tries to kill Sharon, the Succubus again tries to warn Skinner in his sleep and fails. Then when Scully is in danger and Sharon is dying, the Succubus saves Sharon's life and somehow communicates to Sharon the information that Scully is in danger and where to go. So the Succubus repeatedly tries to talk to Skinner but cannot, yet she can communicate information to Sharon. Is it because she is woman? Perhaps it is because she's on the verge of death?
This episode takes place in March 1996. The Succubus has been trying to contact Skinner in his sleep for 5 months, so the Succubus returned in October 1995. The "Anasazi" trilogy takes place in April 1995. The "Piper Maru" two-parter takes place 5 months after the "Ansazi" trilogy, which puts it in September 1995. So the Succubus returned about a month after Skinner was almost killed by Cancer Man; is this when Cancer Man began his "Avatar" discredit scheme? Perhaps he cooked it up then, but he had to wait a couple months so it wouldn't look too suspicious. So why didn't the Succubus warn Skinner about the assassination attempt in "Piper Maru"?
Skinner has been seperated from Sharon for 8 months, so Sharon left him in July 1995. This is after the "Anasazi" trilogy, so it really takes place in a vacuum in terms of Skinner stories. Then again, Sharon said he'd been like that for a while, so perhaps he began acting like that because of the "Anasazi" trilogy, or perhaps even eariler when he was forced to close the X-Files in "The Erlenmeyer Flask".
Historically, the phosphorescent glow is on the men who the Succubus contacts. Yet it's on Sayles' mouth. Does this mean the Succubus tried to possess Sayles to try and warn Skinner, but couldn't because Sayles wasn't near death like Sharon is when the Succubus is able to communicate to her? Then again, there was salvia in there so maybe its also where Skinner... licked her.
Mulder is probably right about Skinner's credit card use being a fraud.
Either the OPR Board is working with Cancer Man on the discredit, or they're just taking the oppurtunity for themselves. Though Cancer Man is seen with them in "Ascension" and they don't mind, they are willing to listen to Scully in "Herrevolk" when she exposes the smallpox enoculation recording system.
Why did the phosphorescent glow disapeer? Either it fades away quickly, or Cancer Man had it removed. For that matter, maybe the material wasn't unidentifyable but Cancer Man made sure that's what Scully was told.
This is one of the few instances that shows Cancer Man in knowledge of an unexplained non-alien phenomena. In "Tooms" he expresses that he believes these things that Mulder talks about, and here he uses one to frame Skinner. This begs the question; shouldn't Cancer Man be researching these X-Files for any kind of potential weapon against the Colonists? Then again, in "One Son" it seems that Cancer Man is more than willing to sacrifice the global population so maybe he's not interested in active resistance.
It's very surprizing that Cancer Man wouldn't know that an air bag can make a composite picture of the driver's face.
X told Mulder that "they" have something on Senator Matheson, like they do on everybody. Perhaps the majority of this blackmail comes from this little prostitute ring that Cancer Man indirectly runs.
So why exactly is Skinner reinstated? Because he killed Air Bag Man? Because of just the air bag face evidense?

WETWIRED

The Run Down:

A man Patnick kills the same smirking man twice, then gets confronted by two cops who are also the smirking man. He attacks the two cops but gets tazored. His vision distorts in electric static and the two cops's true faces are revealed. Patnick is horrified to discover that he has killed his wife.
Mulder meets the Plain-Clothed Man who asked for a meet via anoymous email. He is late because he was asked to make sure Mulder wasn't followed. He hands him an article on Patnick killing his wife and 4 others, and tells him to follow it. He has nothing else; he is just a messenger. Mulder refuses unless he knows who sent him. Plain-Clothed Man says he was told to say more people will die if he walks away from this and leaves.
A Dr Stroman has Patnick under heavy sedatives but it barely affects him. Stroman was called in from DC by another doctor who isn't here. Patnick has a frentic outburst when he sees the smirking man on tv- a Yugoslav war criminal responsible for thousands dead. At Patnick's house are hundreds of video tapes of cable news. As Mulder and Scully arrive, a cable van pulls up and Cable Man removes something from the telephone pole, knocking out Patnick's cable. They review the tapes; the Yugoslav criminal appeared on the tape each night Patnick murdered. Scully watches the tapes all night while Mulder sleeps. She hears Mulder on the phone in the next room agreeing to a meet outside and saying Scully doesn't know. Outside Scully sees Mulder get in a car with Cancer Man and hand over one of Patnick's tapes.
Mrs Riddock is doing her dishes when her vision distorts in electric static. Outside she sees her husband in a hammock with a young babe. She runs out and shoots the man with her rifle. Turns out the man was her neighbor sleeping with his dog. Riddock has hundreds of tapes of home shopping. Mulder sees Cable Man on the telephone pole again and chases him off. Mulder finds a gold cable trapper scrambler. Scully is increasingly suspicious of Mulder.
Mulder takes the scrambler to the Lone Gunmen. It looks like a scrambler to block premium cable, but it doesn't block anything it actually adds a usually invisable signal in the television broadcast. It is of highly advanced design and would be destroyed if you took it apart by design. All they know for sure is its emitting a signal.
Scully nervously calls Mulder asking why he didn't take it Pendrell. She hears clicks and hangs up, then frantically searches her hotel room for a bug. Mulder arrives and has the owner open the door; Scully fires at the door and flees. Mulder calls Margret Scully asking if Scully has contacted her. Skinner is conducting a man hunt but Mulder tells him that he can talk down Scully, she's suffering a paranoid psychosis. Mulder sets the signal for X, but has to go over to the Lone Gunmen. They've found the scrambler stimulates electrical activity in the brain which heightens suggestibility. Americans and Russians have worked on this for decades. Mulder is immune because he is red-green color blind, but this means only a small percentage of male Americans would be unaffected.
Plain-Clothed Man contacts Mulder. He says "they're watching you... you're wasting time. While you're chasing your partner, they're destroying the evidense. Just follow the evidense. If you don't, by tomorrow, the responsible parties will be out of your reach".
Mulder visits Margret Scully's house; she hasn't been answering her phone. Scully is there and puts her gun on Mulder, accusing him of being with 'them' who abducted her. Margret talks Scully down. The scrambler brings out a person's greatest fears, Mulder has determined.
Mulder asks Scully's doc about Stroman's medication for Patnick; it doesn't make sense. Mulder check on Stroman who has left the hospital. The local number he left was the motel Scully was at; Stroman just left and the room is ransacked. There is a Morley's cigarette butt in an ashtray. Mulder tracks a local phone call to a house; outside Cable Man and Dr Stroman are waiting for someone to arrive. Mulder sneaks into a house; he hears two gunshots. He finds Cable Man and Stroman shot in the head, and X standing over them. X says "you're too late... you were told this would happen. You made your choice". Mulder says he didn't know he working for him. X says "I had no alternative. I was being watched too closely. I couldn't risk comprimising myself". Mulder asks why he killed them if he wanted him to expose them. X says "those were always my orders... I was just hoping you'd get to them first". Mulder asserts the experiment was to alter people's behavior and decision-making processes. X says "you think they'll stop at commerce and politics?". X says he failed. Mulder rants how X is a coward who risks his and Scully's life but never his own. X just smiles and walks away. Mulder puts a gun on him. X says "you're risking your life right now. You failed. This is your success? Killing me? The truth is, you need me, Agent Mulder". X leaves.
Mulder and Scully report to Skinner. It is an open ended case with no proof or conclusions; Stroman and Cable Man had false identities. Skinner asks about their killer. Mulder says "he remains an unknown subject". Elsewhere, X gets into a car with Cancer Man. Cancer Man asks "have you completed your work?". X says "all the personnel and hardware have been removed, but Mulder still has one of the devices". Cancer Man says "it proves nothing. What about, Mulder's source?". X says "he's been eliminated". Cancer Man asks "and his source? Who's he working with?". X says "that person remains unknown". They trade uneasy looks.

Plot Points:

Cancer Man orchestrated a successful experiment of a cable television scrambler which emits a signal which brings out a person's worst fears. Only men who are red-green colorblind (like Mulder) are immune to the signal.
Mulder became so enraged at X's manipulations that he put a gun to him.
X is under suspicion and is being watched too closely for him to contact Mulder easily.
X is a direct underling of Cancer Man, who is responisble for the coverups (including murders) of Syndicate experiments.

Analysis:

Stroman claims that Patnick was able to shrug off heavy sedatives, but he was probably lying.
So Patnick and Riddock record hundreds of hours of television. Was this a cause or symptom of their being affected by the signal? Since the conspirators had to manually put a scrambler in each person's box its most likely a symptom. Of course this means that being affected is a gradual thing that takes place months; Scully was affected so quickly because she saw the equivilant of months of the signal.
This scrambler is definitly just advanced human technology, nothing alien involved.
Red-green color blindness is a condition that affects men almost exclusively, and only a small percentage of men.
Gee, isn't it CONVEINENT that Mulder is red-green color blind and this makes his immune to the signal!
Plain-Clothed Man tells Mulder that 'they' are watching him; that means 'they' see him meeting with Plain-Clothed Man! No wonder he ends up dead by the end of the episode!
So X is under suspicion by someone in the Syndicate. Could this be related to First Elder's suspicion in "Apocrypha" that they have an information leak? This leak is Krychek, but Well-Manicured Man didn't neccessarily tell his fellow Elders. However, "Apocrypha" took place in September and this episode takes place at the end of April, almost 7 months later! They're probably unconnected.
Of course, this suspicion of X pans out in "Herrenvolk" when First Elder tells Cancer Man they have an information leak which is ultimately revealed to by X and he gets killed for it.
So X was under orders from Cancer Man to kill Cable Man and Stroman when the experiment was done. While this makes sense, it must not breed confidense in the lower ranks of the Syndicate!
So X says this mind-control ability will go beyond commerce and politics. So what is it for? Could this experiment be connected to Colonization, perhaps making people just stand by and accept Colonization? Of course, only so many people get cable and the Syndicate would have to produce millions of the scramblers. And even still, what about the rest of the world?
Then again since we never hear from this device again, it's not that important to worry about! Since this experiment was successful, it's amazing that the Syndicate doesn't use it!
X smiles when Mulder calls him a coward because in "731" X risked his life to save Mulder and the exploding boxcar.
When Mulder puts a gun on X, X says he's risking his life now. Why? Because X would kill him for putting a gun on him? In "End Game" he says he tells Skinner he's killed men for doing far less. Or because someone is watching them and will shoot Mulder to protect X? If so, this observer would have to a compatriot of X and not a Syndicate stoodge- Plain-Clothed Man?
Cancer Man seems suspicious of X slightly at the end.

TALITHA CUMI (part 1 of 2)

The Run Down:

At a resteraunt, a disgruntled worker Muntz holds the patrons hostage. Jeremiah Smith calmly talks him down, but a Swat team shows up and Muntz and others get fatally shot. Smith somehow heals their wounds with the palm of his hand. Mulder and Scully soon arrive to investigate; Smith gave his name and a false address to a detective then disapeered before his eyes. Another man in identical clothes was there instead who walked away. Muntz says it was God.
Quonochontaug, Rhode Island- Cancer Man meets Teena Mulder at the abandoned Mulder summer home by the sea. Cancer Man says they used to have a lot of fun together here with the children, he and Bill would water ski. Cancer Man alledges that they had an affair, but Teena says "I've repressed it all". Cancer Man says he came here to ask her to remember something very important. As someone far away photographs them, they argue heatedly about something then Cancer Man leaves. Soon Mulder gets a call from Skinner; Teena is in a hospital and has had a light stroke. Someone called it in anymously; Teena can't talk but writes out a message to her son: PALM. Mulder suspects a connection to Smith, but Scully says Teena's speech center is probably just altered. Teena falls into a coma soon afterwards, and may never regain conscious again.
Cancer Man and several suited men grab Smith from his work cubicle at the DC Social Security Administration. Smith is locked in a prison cell, with his face all strapped up.
Mulder visits the Mulder summer home, where X is waiting for him. X says "The Cancer Man" was here with his mother, and gives him the photos taken. X said they had an argument, which shocks Mulder. X says "you seem surprized. Surely you were aware they knew each other, or what brought them here together". Teena collasped after Cancer Man left, and X saved her life by calling the hospital. X doesn't know what they talked about, "I was forced to keep a discreet distance". Mulder says he must have some idea or he wouldn't have followed him. X says "he wants something from her. Something she may have kept in this house. Unless you know another reason they would have chosen to meet here". When Bill and Teena divorced, Teena vowed never to return to this house again. X says "it could be something very old. Certainly something very important". X pushes Mulder for what it is, but he doesn't know.
Scully finds Smith at the FBI Building, he has come to turn himself in after hearing how he fled a crime scene. Smith recounts talking down Muntz to Scully and Skinner, but doesn't remember anything after that until he showed up for work the next day. Smith asks to be released, and Skinner lets him go.
Mulder ransacks the Mulder summer home, and eventually finds a Glimlet in a lamp. It is connected to a tube-like device.
Cancer Man visits Smith in prison and releases his face straps. Cancer Man says "this now becomes a responsibility, the thing I'm now called upon to put right and put down. Certainly you expected nothing less". Smith says "I'm not ashamed of my actions". Cancer Man says "you're not allowed the luxury of human weakness in penitence. You're not allowed to put your indulgences ahead of the greater purpose". Smith says "I no longer believe in the greater purpose". Cancer Man says "then your fate is just". Smith says "my justice is not for you to mete out. You may have reason, but you have no right, you have no means either". Cancer Man says "you presume to dictate duty to me? Have you any idea what the cost of your actions is? What their effect might be? Who are you to give them hope?". Smith says "what do you give them?". Cancer Man says "I give them happiness and they give us authority". Smith says "the authority to take away their freedom under the guise of democracy!". Cancer Man says "men can never be free, because they are weak, corrupt, worthless and restless. The people believe in authority. They've grown tired of waiting for miracle and mystery. Science is their religion. No greater explanation exists for them. They must never believe any differently if the project is to go forward". Smith says "at what cost to them?". Cancer Man says "the question's irrelevant, and the outcome inevitable. The date is set". Smith morphs into Deep Throat and says "at what cost to them for your own selfish benefit? How many must die at your hand to preserve your stake in the Project?". Cancer Man is shaken but says "I'm not impressed by your miracles or moved by your trickery. Your justice will be meted out". Smith/Deep Throat says "by whom this time and by what tools?". Cancer Man says "by those who possess the tool of your destruction" and leaves.
Mulder demands Cancer Man's identity and location from Skinner. Skinner says he doesn't know his name and he can no longer contact him. Mulder asserts he's trying to kill Smith, and learns about Smith's visit to the FBI. Mulder and Scully pick up Smith at work for further questioning, but he disapeers into a crowd by morphing into a bearded man.
Cancer Man vists Smith again, saying "it's only a matter of time now". Smith says "you put me in a cage, within a cage. Why are you so afraid of me?". Cancer Man says he isn't. Smith says he is, "you live in fear. That's your whole life". Cancer Man says "you don't know anything about me" but Smith says "I know everything about you. You think the miracles I preform are the extent of my power?". Cancer Man says "you think your God? You're nothing but a drone, a cataloger, chattel!". Smith says "what you're afraid of is, they'll believe I am God". Cancer Man says it doesn't matter, "most of them have ceased to believe in God, because God presents them with no miracles with which to earn their faith". Smith says "you think when man ceases to believe in miracles, he ceases to believe in God? You rule over them in God's name!". Cancer Man says "they don't believe in Him, but they still fear him. They're afraid not to because they're afraid of freedom. [We give them happiness], we appease their conscience. Anyone who can appease a man's conscience can take his freedom away from him". Smith morphs into Bill Mulder and says "and if you can't appease their conscience you kill them. But you can't kill them all, you can't kill their love, which is what makes them better than us, better than you". Cancer Man is shaken, and says "I'm not one of you!". Smith/Bill Mulder says "all you want is to be a part of it, is to be one of the Commandants when the Process begins". Smith says he is dying of lung cancer, and Cancer Man knows its true. Soon Smith/the bearded man arrive, morphed into his true form The Pilot. He enters the cell with a Glimlet to kill Smith, but finds the cell empty.
A distraught Mulder finds Cancer Man outside Teena's room at the hospital. He angrily puts a gun on him, but Cancer Man calmly says he's here to see how Teena is doing, "I've know your mother since before you were born, Fox". Cancer Man he'd gone to see her recently, she had contacted him because he had possible information on Samantha's location, but the man who had that information has disapeered. Mulder says he has what he wants, but Cancer Man doesn't want anything. Mulder leaves.
Scully checks SSA files and finds 4 more identical Smiths working in Seattle, California, Chicago, Miami, and New York City.
X meets Mulder in a parking garage, demanding the weapon. X says "it's of no value to you. [To me], when the time comes. When the truth is finally determined, its value will soar". Mulder asserts its the only weapon that can kill "them", X confirms a gunshot won't do. X says they will kill Mulder for the weapon, even if they have to martyr him for it. Mulder says "let me get something clear here. What we're talking about is Colonization. The date is set, isn't it?". Mulder refuses to give him the weapon, and X attacks. A brutal fist fight ends in a stalemate when they both get to their guns. X is very nervous, and says Mulder is a dead man, "one way or the other".
Smith arrives at Scully's apartment, offering information. Scully carefully lets him in. Smith offers information "your partner has been seeking. It concerns an elaborate plan, a Project, and his sister". Smith has never met her before, the man she met was an imposter sent here to kill him. Scully calls Mulder, and they agree to a meet in a secluded lumber yard at night. Mulder holds the Glimlet on Smith and keeps Scully behind him. Smith offers to explain everything, but first Mulder wants him to visit his mother. Smith agrees, but The Pilot drives up and walks up to them holding a Glimlet while Mulder is lost as to what to do.

Plot Points:

Enter Jeremiah Smith(s): some kind of Hybrid who can heal sickness with the palm of his hand, morph his appearance, and has telepathy. 5 identical Smiths work at the Social Security Administration across the country. They are just drones and catalogers, and are not allowed to live free lives but work in slavery for the Project. This Smith has gone renegade by healing some people in public and offering the truth to Mulder. Cancer Man has dispatched The Pilot to kill him.
Cancer Man used to spend summers with the Mulder family, and may have had an affair with Teena before Fox's birth.
Teena Mulder has had a stroke and is now in a coma.
X keeps Cancer Man under surveillance, but Cancer Man's security forces him to keep a distance.
A Glimlet was sitting in a lamp at the Mulder summer house; Teena knew about it.
Skinner can no longer contact Cancer Man. He doesn't know Cancer Man's name.
Smith reveals Cancer Man's inner nature: he lives his life in fear. All he wants is to be a Commandant when the Process begins.
Cancer Man says man must cease to believe in God for the Project to go forward. He holds disdain for man because he fears freedom so he allows Cancer Man and God to rule over them in fear, because science is their religion now.
Cancer Man had lung cancer, but the renegade Smith healed him in return for his freedom.
A Glimlet is the only way to kill the Hybrids and aliens. Cancer Man doesn't have one and must call in a Pilot to use one. X is desperate to get the Mulder Glimlet from Mulder.
X gets into a fight with Mulder for the Glimlet. X threatens Mulder's life.
Mulder has now guessed that the Project is about the Colonization of Earth.
The renegade Smith offers to heal Teena and reveal the Project to Mulder, but The Pilot has found them.

Analysis:

Smith's healing ability is very strange; it even sucks the blood out of the shirt of Muntz! In reality they just played the film of blood flowing backwards, but how is this supposed to really work? Reversal of time? Hope not!
So Cancer Man hears about a Smith using his powers in public. He must be killed, but Cancer Man doesn't have a Glimlet. He's afraid to have to contact the Colonists because it's a sign of weakness, so he contacts Teena, hoping to get the one that the Mulders had. That doesn't work, so he then contacts the Colonists and asks them to send over a Pilot.
Here begins the tease that Cancer Man is actually Mulder's biological father! This silly thread runs up to "Redux II" when Cancer Man almost dies and goes into hiding. When he returns in "The End", he is now adversarial towards Mulder.
Just why did Teena get so upset about Cancer Man asking about the Glimlet? She was really fuming there, but all he wanted was a Glimlet! Perhaps she knows its importance and wants to keep it for self-defense since she probably knows about Colonization. Of course the other big question is, why didn't she tells Mulder about it? In all her apperances, she doesn't seem very caring about Fox.
Then again, after her stroke she DOES tell Mulder about the Glimlet. Is it because she didn't want to die without Mulder getting it, or because she finally realized that Mulder is heavially involved with ferreting out the Project and he needs it for self-defense. Or maybe it was simply so Cancer Man couldn't get it.
Why didn't Cancer Man just have some of his goons ransack that house if he knows the Glimlet is in there? Probably his innane protection of the Mulders, which is a character trait we see again in "One Son" where he's willing to sacrifice humanity just to prevent having to kill his wife Cassandra. And if it wasn't that important, why did he put Teena through the stress to begin with? Again, maybe he wanted a reunion with Teena.
Did X take those photographs himself? He later says that he did to Mulder.
Does X always Cancer Man around when he's free or was it just because of the connection to Teena Mulder and the Smith affair?
So apparantly, Teena meant to write LAMP but her stroke messed up her speech center so she said PALM instead, which by an amazing conicidense an derivation of Lamp!
Apparantly those face straps on Smith prevent him from morphing somehow.
Why would X call Cancer Man "The Cancer Man"? Surely he knows his real name as he's one of Cancer Man's top goons! If he's keeping the name secret from Mulder, then where'd he get the name Cancer Man? Mulder came up with the name in "One Breath" and Scully uses it in "Wetwired" so it suggests that X/the Syndicate has Mulder under regular surveillance, but of course we already know that from many many episodes.
Just why is X so desperate for a Glimlet? He thinks it will be important come Colonization time, but how much good is only one going to do? Could it have something to do with his secret agenda against the Syndicate?
In X's first meeting with Mulder, he is obviously trying to grill Mulder about the Glimlet. Most likely X just guessed that Cancer Man trying to get a Glimlet from Teena because of the recent Smith affair. Because if he already knew there was a Glimlet there, he would have ransacked the house to get because he is very desperate to get it here.
Apparantly Cancer Man calls in The Pilot on the Colonist Radio in between his two scenes with Smith. So since the FBI-Smith appears before the first Cancer Man-Smith scene but after Cancer Man arrests Smith, who is this imposter? It is assumed that it was The Pilot, but most likely The Pilot hasn't arrived at Earth yet! Maybe its one of the other 4 Smiths who Cancer Man called in to coverup the situation before calling in The Pilot for the Glimlet execution.
So the Colonists do not usually have a direct presence on Earth, nor are there any Pilots on Earth. When the Syndicate runs into a problem it can't handle, they must call the Colonists for help. They do so with a thus-far unseen or unheard-of Colonist Radio, which we indirectly see them use in "One Son" both in 1973 and in 1999, so that must be what Cancer Man uses here.
Then again, for The Pilot to show up within a few hours of the call must mean that he's already in America. Considering the last time a Pilot was called in (in "Colony") he had to crash his ship in the Artic, take a few days to be taken to America, escape a hospital, all before he could begin his hunt.
In reality, the Glimlet is attached to a steam tube which runs up the arm of the actor, which allows the blade to hiss out. Then in later scenes the actor holds just the Glimlet without the hose (incidentially when The Pilot walks into the prison cell you can see the steamtube running out of his sleeve!). When Mulder finds the Glimlet here, it is connected to the steamhose. He disconnects it, and extends the blade without the steamtube attached (not in reality). So what was the purpose of this pseudo-steamhose? Mulder apparantly doesn't keep this section because we never see it again! Then again, perhaps it was just some connection to the lamp.
Cancer Man considers Smith to be sub-human, not worthy of rights or freedom.
So Cancer Man is afraid of one of the Smith Hybrids using his alien powers because it will give hope in man and make him believe in miracles again. For some reason this would be adverse to The Project. Why? If the Colonists are going to forcibly take over humanity, what does it matter whether or not they believe in miracles and God? Perhaps he means that man can't believe in miracles because then he'll believe in aliens and the aliens' existance can't be exposed before Colonization begins or else the Project will be useless (because humanity will be expecting it and can prevent it by stopping the Syndicate's operations).
So this renegade Smith has turned against his purpose, The Project, and has disdain for the Syndicate because they are selfish collaborators who would kill humanity to save their own lives. What exactly led him to this point of view? Surely it had nothing to do with the Muntz shootout, or maybe it was the catalyst to his outlook; he didn't want those people to die. In any case, does this mean the other 4 Smiths are likely to go renegade too? Of course in the next episode "Herrenvolk" the other 4 Smiths promptly disapeer, most likely murdered by Cancer Man for just that possibility!
Cancer Man is disgusted with man because science is their religion, and they're afraid of freedom and prefer to live in fear. Ironically, he just about describes the point of view of Scully! Science is her religion! Does this mean that he holds great disdain for her? Don't be confused with his claim that he spared her life (during the abduction) because he liked her, as he told Mulder in "One Breath". She would have been returned anyway.
By Smith's morphing, it proves once and for all that Cancer Man ordered the deaths of Deep Throat and Bill Mulder, and these two were very close friends of his.
So Cancer Man is so defeatist about humanity because he knows it only has about 17 years left to live ("The Red and the Black").
Considering that Mulder saw a morphing alien in "Colony" and "End Game", its amazing he doesn't pick up on Smith's morphing ability since he sees news footage of Smith turning into a different man in the same clothes after a brief obscure shot. That way, the faux-Smith that he picks up at the SSA gets a chance to escape because Mulder didn't think to grab anyone with the same clothes as the faux-Smith... because he's an idiot!
Cancer Man lives his life in fear? Fear of what? Of humanity's fate? Of the truth being discovered and him getting burned at the stake?
Cancer Man called Smith a "chattel": it means slave or cattle.
So Cancer Man's big goal in life is to be one of the "Commandants" when "The Process" begins. The Process must be the mass infection of humanity with Black Oil, thus creating (as far the Syndicate knows- they learn otherwise in The Movie) a slave race. So Cancer Man wants to be one of the few 'free' humans who will rule over the new slave race. Wow, in "One Son" we learn he just wanted to find a way to resist the Colonists, get humanity to survive, and be reunited with his wife Cassandra!
Obviously in return for healing him of lung cancer, Cancer Man let Smith escape from prison without telling The Pilot, though The Pilot continues to hunt Smith so Cancer Man didn't call him off or anything.
Cancer Man is pretty clever; he sees that Mulder is a few ticks away from blowing his brains out so he teases him with information about Samantha which promptly calms him down! Of course we learn it was true in a way, Smith did have knowledge about Samantha, that her Hybrid clones were being used to tend a Project farm in Canada. If Cancer Man still had Smith, perhaps he would have produced a Hybrid Samantha to manipulate Mulder. He does this exact same thing in "Redux II"!
Cancer Man says he doesn't want anything from Mulder; this is because he already has a Glimlet by calling in The Pilot.
So Smiths come in identical clones. Other identical Hybrid clones: the Adult Samanthas in "Colony", "End Game", and "Redux II"; the Gregors in "Colony" and "Endgame"; the Adult Kurts in "Memento Mori"; the young Kurts and Samanthas in "Herrenvolk". Of all these identical Hybrid clones, only the Smiths can morph, heal, and read minds. All of them have the green alien retrovirus blood and can only be killed with a Glimlet. Yet Smith is afraid of The Pilot (thus The Pilot is more powerful than him), even though he has a lot of The Pilot's abilites! Perhaps he doesn't have the all-important super strength, since a bunch of humans arrest him at one point. We never again see a Hybrid clone that can morph other than Pilots, so maybe its a dropped story concept.
It seems really incredible that a Glimlet is the ONLY way to kill a Hybrid, to the point that Smith must sit in a prison cell while Cancer Man calls in a Pilot. What about decapitation? Asphyxiation? Gunshot to the head? Gunshot to the neck? For that matter, is the Glimlet some kind of alien kryponite metal? Or would a plain old ice pick at the base of the neck do it too?
X is most likely lying to Mulder about how they'll kill him for the Glimlet; they don't even know he has it! Then again Mulder told Cancer Man he has what he wants, but maybe Cancer Man assumed Mulder didn't know what he was talking about. Even so, it's doubtful since they can just call in a Pilot if they need a Glimlet, as besides as of "Mento Mori" Cancer Man has a Glimlet himself without having to contact the Colonists!
At least, we learn the true thrust of the series in some throwaway dialogue. The Colonization of Earth. Mulder now knows of it.
This is the end of the Mulder-X relationship; they never see each other again alive.
After the ordeal of "The Blessing Way", it was very clever of Scully to be so cautious about Smith arriving at her apartment door.
So how did The Pilot know about the lumber yard? Obviously the Syndicate is tracing Mulder's cell phone and relaying the information to The Pilot! In fact, considering the number of times this happens its amazing that Mulder gave the location over the cell phone!

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