X-Files Mythology Guide Season Five

Mythology Guide: Season Five

REDUX (part 2 of 3)

The Run Down:

24 Hours Earlier... Mulder sits in his apartment crying, realizing his hope of finding aliens and being reunited with Samantha is false. He considers his loaded gun when Kritschgau calls saying "there's a matter of security. Something I hadn't anticipated. Just after I left your apartment. Just after our last conversation, I was followed by people... they may be listening, they may be watching you". Mulder hands up and notices a ray of light from the cieling; a small surveillance camera is watching him. Mulder races upstairs and busts in the apartment above his; Ostelhoff is inside burning papers, the room is filled with video equipment. Mulder tries to put out the fire, and Ostelhoff grabs his shotgun. A shot rings out, and someone closes the door.
Mulder visits Scully at her apartment; there is a body in his apartment with a gunshot wound to the face, he's been under electronic surveillance for at least 2 months (including July and October). Mulder now has Ostelhoff's DoD Advanced Reserach Facility identification card. Ostelhoff tried to burn phone records where he called the same PBX operator at the FBI 17 times; Mulder asserts this hoax conspiracy also lies in the FBI, they have to lie to the FBI in order to find out which of them is them is the traitor.
Scully ids the body at Mulder's apartment. Skinner asks how she could since it was a shotgun blast to the face; she says he was wearing the same clothes he was earlier. Skinner tells her Section Chief Blevins wants for questioning about information she has. Scully meets with Skinner, Blevins, and Senior Agent. Blevins says the DoD has told them one of their employees gave her classified information, he asks if "he provided evidense" about the alien body hoax and conspiracy. He asks what he told her, and what his name was. She ids Kritschgau from a surveillance photo from Mulder's apartment. Blevins has assembled a "joint FBI panel" on the matter.
Mulder enters the Advanced Research Facility using Ostelhoff's ID card, and runs into Kritschgau in the lobby. Kritschgau is very nervous, and pulls him into an office. Kritschgau says that ID card has Level Four clearance; "you have access to everything, things I don't, things I can only tell you about" including the cure for Scully's cancer.
Cancer Man breaks into Mulder's apartment and looks at a picture of Mulder and Samantha as children. He sees the cieling peephole.
Scully checks the phone records; of five consecutive calls per day, they were all transfered "to an executive level extension, it's a branch extension. It could be any of them at that level" including Skinner. Scully gets a call from the man who analyzed the ice core sample.
Kritschgau gives his speech: Level Four "is a biological quarantine wing. It houses a series of labs and medical facilities, and an elaborate facility for the storage of mass quantities of DNA" from almost every American born since 1945, anyone who's ever given blood or tissue to a government doctor. The flying saucer story was invented by the military after WWII to distract the public from their nuclear annihilation policy. Oppenheimer knew of it, but he was silenced. The Cold War became an excuse to spend money on the military-industrial complex, while creating a public paranoia of Russia to distract them from the military. Roswell '47 gave the military the perfect distraction so they built it up, and every supersonic experimental aircraft (which first appeared in '47) were UFOs, "when the abduction stories started up, it was too perfect". There was a misstep using devealopmental germ warware in Korea, which the Soviets and Chinese learned and the UN got pissed. But it was "nothing like what we and the Russians have now. The bio-weapons used in the Gulf War were so ingenious as to be almost undetectable. Developed in this very building". The abduction stories are "citizens taken unsuspecting and tested. A classified military project, above top-secret and still ongoing". Mulder says he's seen aliens, but he says "you've seen what they wanted you to see". The alien body hoax was made to be so perfect it would be believable but never proven, "the timing of the hoax was planned so Scully wouldn't be alive to do the examination". Mulder asks why he went along with it, he says "I paid the price. When my son came back sick from the Gulf War, that was my retribution" he hopes there is a cure in Level Four for his son.
Cancer Man meets First Elder at the racetracks, who is accompanied by Quiet Willy. Cancer Man contacted him, he says "it seems I've been left out of the loop. You've been watching Mulder. You had a man on him. No one bothered to inform me of this". First Elder denies knowledge, but Cancer Man says "I will not be cut out like this. You need my expertise. Is this being run from the DoD? I've always kept Mulder in check. I put this whole thing together, I created Mulder". First Elder says Mulder killed himself, "our FBI source confirmed it this morning... Mulder was an asset. Without his partner you may have underestimated his fragility". Cancer Man says "I've never underestimated Mulder, I still don't" and leaves.
Scully meets the ice doctor; the chimera cells found in the ice were put in fetal bovine serum and the cells began to divide. This is an animal characteristic, but they are not classifiable. They underwent miotic cell divions and went through the stages of morula, blastula, gastrula. The cells began "somatic devealopment" to begin a new life form, "an unidentified microscopic lifeform"which Scully thinks will prove or disprove alien existance. She suspects it is "biological proof of this connection to the cancer invading my body to a virus living inside this organism to which I had been exposed during my abduction 3 years ago". These unclassified chimera cells "were full of virus".
Mulder enters the Level Four area and Kritschgau gets arrested for questioning by MPs. It is a long hallway of locked doors, but he picks a door lock to a large chamber holding 56 dead Grey aliens like the faux body. Through a small connecting hall he finds a locked room full of 12 pregnant unconsious women with grid lights being played over their bellies and a flashing light everywhere. Mulder follows a long connecting tunnel which takes him to the Pentagon basement, so the security door that Cancer Man used in "The Pilot" and "The Erlenmeyer Flask". His ID card opens it, and inside a colossal chamber of evidense folders. At the back is a giant antiquated filing system of index cards. He finds Scully's index card (id number 2317-616) which lists three long numbers; in red ink are two numbers which begin with SEP and ADG, and the number MN1068-06.. He also finds Kritschgau's son's card but it is blank. Kritschgau's card has the three long numbers but no red ink. Mulder looks up Scully's code number and finds a box of small metal vials. He takes one and leaves. MPs alert Cancer Man to 'Ostelhoff's access to the Pentagon and show the security view in the Vault, but Cancer Man lets him escape.
Scully sees Skinner following her; he tells her he has pathological reports saying the body is not Mulder and says her lie about it is on record and she'll get in more trouble if she continues to lie. Scully is very suspicious of him and accuses him of working with the DoD.
Scully isolates the DNA from the virus in the chimera cells and compares them with the DNA which she thinks caused her cancer. It's a match; "my DNA hybridized with the viral DNA from the cell culture" which means she has the DNA from the unclassified chimera cells in her body. She says she was exposed to the virus and chimera cells and it gave her her cancer.
Scully testifies before the FBI panel (the "Gethsemane" scene). Skinner enters the conference room with the pathological reports. She offers evidense that she was given cancer by the same chimera cells from the hoax-body and the same people responsible, one of whom is in this room. Her nose begins to bleed and she collaspses in Skinner's arms.
Mulder takes the vial to the Lone Gunmen. Inside is a clear liquid which they pour out and analyze; deionized water and nothing more.

Plot Points:

Scully lied to the FBI panel to cover Mulder while he broke into the DoD Advanced Research Facility.
Mulder's apartment has been under surveillance for at least two months and the observers have called someone at the FBI executive level (possibly Skinner) almost everyday to report.
Mulder uses a murdered DoD employee's ID card to break into the Advanced Research Facility Level Four and the Pentagon vault and steal Scully's cure from it. Cancer Man allowed him to do it.
DoD Advanced Research Facility Level Four: a biological quarantine wing which stores DNA from almost every American born since 1945. There is also a chamber of faux-Grey bodies, a chamber of unconsious abducted pregnant women with grid lights playing on them, and an underground tunnel to the Pentagon Vault.
The Pentagon Vault has an antiquated filing system. Scully has a card and it lists her cure which is also in the Vault. The cure is a metal vial, but inside is only deionized water.
Kritschgau's son became sick in the Gulf War but at the Pentagon Vault his card lists no cure. According to Kritschgau, the germ warfare used in the Gulf War was devealoped at the Advanced Research Facility and modern germ warfare from the US and Russia is virtually undetectable.
Someone at the executive level of the FBI is a Syndicate pawn, possibly Skinner. Scully thinks its Skinner.
First Elder is responsible for the surveillance of Mulder but he denies it to Cancer Man.
Cancer Man claims to have created Mulder.
The chimera cells from the faux-body are full of a virus whose DNA is identical to her DNA; she was infected with the chimera cells.
Scully offers proof to the FBI panel that she was exposed to the chimera cells, but she collapses from her cancer.

Analysis:

So Kritschgau never considered that Mulder would be under surveillance, even though he gives this whole tirade about how 'they' created Mulder and use him as a pawn?!
So Mulder shoots Ostelhoff first, killing him. Then he uses Ostelhoff's shotgun to shoot Ostelhoff in the face after his death, and switches clothes with the body to give the impression that it was him who died.
Mulder says he's been under suveillance for at least two months after reading the burned reminents of Ostelhoff's papers. Scully later shows us these papers, and they include July and October. First of all, why would Ostelhoff have a phone record of his own calls there? Second, Mulder says two months seeing the same papers, yet it would have to mean that the surveillance began at the very end of July and the episode takes place at the very end of October. Yet, this is a season finale/premiere and these episodes historically take place around April and May!
Skinner produces a picture of Kritschgau which is obviously from the cieling camera in Mulder's apartment, but Scully doesn't make note of this fact. Then again, maybe that's why she begins to distrust Skinner!
For Scully to mistrust Skinner is ridiculous; he re-opened the X-Files in "One Breath" and saved their jobs and lives in "Paper Clip". He took a bullet for Scully investigating her sister's murder in "Piper Maru". He sacrificed himself to Cancer Man to cure Scully in "Memento Mori", but then again his subsequent work as Syndicate stoodge in "Zero Sum" could encourage doubt.
So if Kritschgau doesn't have access to all the things he talks of, how in the hell does he know about them?! Obviously he's done some snooping around, perhaps this is why his theories are so far off from the truth, because he's filling in a lot of blanks from proof.
Level Four is a biological quarantine wing, just like the biological quarantine wing of the Lombard Facility which housed the harvested ova and Hybrid birthing tanks in "Memento Mori"! A nice connection!
Kritschgau says Level Four houses a giant DNA database, but we never get to see it, then again there were many locked doors Mulder didn't go through.
This giant DNA database, is it the same thing as the Strughold Mine complex in "Paper Clip" which housed thousands of tissue samples? Sounds like it. And is it like the billion-entry Smith database in "Herrevolk" which catalogues the protein markers of people with smallpox innoculations? Less likely so. Perhaps after Mulder saw the Strughold Mine complex it became comprimised so all the files were moved to the DoD Advanced Research Facility.
Kritschgau gives the most realistic theory on how they get this DNA; every government doctor since 1945 has been sending blood and tissue to this database. This is much more realistic than taking it during only smallpox innoculations and from abductees!
Perhaps the DNA database was the index card filing system Mulder saw, but Kritschgau was referring to actual DNA most likely.
Surprizingly, Kritschgau knows about the Syndicate UFOs and their use in abducting people. That's top level stuff!
What is this germ warfare misstep in Korea? Obviously it was during the Korean War of 1949-1953 as I recall.
Kritschgau says the alien body-hoax was timed so Scully would be dead before she could examine it. This sounds really over the top, like Scully is the only doctor Mulder could get his hands on, hell he got Arlinsky!
Obviously First Elder was responsible for Ostelhoff despite his denials otherwise.
So First Elder set up a secret surveillance on Mulder, which seems as a precursor to the alien body-hoax which would thus mean that First Elder was behind the whole body-hoax and not Cancer Man. Which would mean that First Elder was trying to make Mulder go public, then get completely discredited. If its true that Kritschgau was an unwitting pawn as well, then First Elder was behind that as well, with the hope of getting Mulder discredited and no longer believing in aliens, perhaps even to commit suicide though that seems a bit hard to predict.
In all this it seems that First Elder has more contact with the Department of Defense than Cancer Man, perhaps back in the '40s and '50s First Elder was working not in the State Department like most them but in the DoD.
Cancer Man says he created Mulder. This gives credence to Kritschgau's theories, but it most likely means that Cancer Man has guided Mulder to become an unwitting pawn and advanced agent for the Syndicate.
The chimera cells underwent miotic cell divions and went through the stages of morula, blastula, gastrula. The cells began "somatic devealopment" to begin a new life form. Morula is an early stage of cell division, a precursor to the blastula. Blastula and gastrula are the devealopment of an embyro, in other words the devealopment of animal life. Plant life doesn't have this. Somatic devealopment could mean the creation of a covering, skin. So the chimera cells began to create an embryo with skin!
When Scully says she was abducted three years ago, she must rounding off some. She was abducted in "Ascension" which took place in August 1994, and this episode takes place around the fall of 1997, which is the space of about two and 2/3 seasons.
So these chimera cells are full of virus. Does this mean the Black Oil virus? In "The Erlenmeyer Flask" Scully sees an alien gene, which is a plant-like alien bacteria with an alien virus inside it. In fact, these things sound absolutely identical since the chimera cells are just Hybrid cells! Why doesn't Scully bring this up?
56 dead Grey aliens? There were around 7 aliens in the roughly 8 rows in the room. A head count got 54, but it was very obscure.
Since that grid light is only played on the bellies of the pregnate abducted women, it must involve the gestation of the Hybird baby.
The connection between the two rooms suggests a connection between the Grey bodies and the abducted pregnant women. Perhaps this local abduction center (we see another in "Memento Mori" which births young drone Kurts) produces only Grey bodies, for the use of alien hoaxes. Since there were only 12 women, it makes sense that they would not need many women to produce alien bodies, since they only use them so often. So the fact that there were 56 alien bodies suggests they are slowly getting a surplus of alien bodies since they don't have much need for them.
These women must be in a coma or something for them to have to be guarded at all. When Scully is returned she's in a coma, yet she has memories of her abduction with the Allentown women. We've speculated in "Memento Mori" that abducted women are kept unconsious throughout their pregnancy so they never know about it. It makes sense here; when the women get pregnant they are put into a coma, then taken out of it after their give birth.
Come to think of it, Scully was returned in a coma but all the other abductees (the Allentown women, Cassandra Spender) get returned just fine! Why the difference? Maybe because Cancer Man wanted Mulder to suffer a bit over it.
As for that flashing strobe light, perhaps it's that radiation treatment!
Where did the connecting tunnel to the Pentagon connect to in the Advanced Research Facility? Perhaps Mulder picked the lock into the pregnant women room and in there was the door to the connecting tunnel. Did he try to wake up one of the women? Did he try to palm some of the stuff they were being treated with?
On the index cards, there are three long numbers. Scully and Kritschgau have them, but Kritschgau's son doesn't have them. Does this mean after serving in the military he's never given any blood or tissue? The numbers might represent the smallpox innoculation protein tag since Kritschgau and Scully have them but Kritschgau's son doesn't (he's not old enough to have had a smallpox innoculation!). Then again Scully has a number reading SEP in red ink, and we know from "Herrenvolk" that SEP means smallpox erradication program, which gave the Syndicate their protein tags. Hmmm...
So what does ADG stand for on Scully's card? It probably involves the fact that she's given birth to a Hybrid.
Why does Scully's new Implant have a specific serial number? Does this mean that only that one Implant would work for Scully? More likely it is merely for inventory purposes, for example in "Patient X" we learn the Implants can make the host drawn to a place, a lighthouse so maybe the Syndicate wants to know who has what Implant so if necessary they could 'draw' them in. Then again, it appears that the Colonists but not the Syndicate possess this ability, so perhaps it is a Colonist order.
Krtischgau's card has no red ink; this means he's never been abducted or birthed a Hybrid (duh!).
Why does Mulder only take one vial? Why not take ALL of them? For that matter, he has access to all this top top secret stuff, and he doesn't take any of it! He should have his coat pockets stuffed with stuff!
Where exactly does Scully get this DNA of her cancer? Does cancer have DNA, wouldn't the DNA be the same as hers or it is mutated somehow? Perhaps she refers to the branched DNA that she's had since her abduction ("One Breath"). But if this DNA is identical to the DNA of the virus in the chimera cells, doesn't this mean that her branched DNA is Black Oil DNA?
So apparantly Scully learns here (unwittingly) that she has Black Oil DNA in her blood. In "The Beginning", Scully learns that every human has Black Oil DNA in the 'junk DNA' which lies inactive in all humans. So her discovery isn't from her abduction, it was just always like that. Shouldn't she have made this discovery though?
And if this virus in the chimera cells isn't Black Oil, what is it?
So Scully officially presents the proof that she was infected with chimera cells which gave her cancer. Yet we never here anything from this! Of course that's par for the course, no matter how much trouble Our Heroes get in to or what evidense they briefly discover it all falls into a black hole after the episode's over!

REDUX II (part 3 of 3)

The Run Down:

Mulder visits Scully at the hospital and runs into Skinner. She went into hypovilemic shock, she's dying. Mulder gets enraged and attacks Skinner, who hauls him away. Skinner brings Mulder to see Blevins and Senior Agent. Blevins and Senior Agent say this is becoming a murder investigation and ask why Scully lied to them. Skinner later tells Mulder he's been holding the forensic evidense on the body for him but had to arrest him at the hospital; the body has a pistol head-wound then a post-mortum gunshot face-wound. Mulder tells him Scully lied because there is a mole in the FBI, connected to those who gave her cancer, but he doesn't know who.
First Elder and Quiet Willy are the horsetrack; First Elder is watching a televised Senate Subcomittee Hearing on Human Cloning. The senators are pushing for no limits to it, saying it is not possible yet anyway. Cancer Man shows up; First Elder knows Mulder is alive and that Cancer Man let him escape the Advanced Reserach Facility. First Elder says "we're too vunerable. Our man in the FBI is exposed, what Mulder may have seen could expose our plans". Cancer Man says Mulder needs help and they can give it to him in return for "his new loyalty. To us... Mulder's much more valuable to us alive". Cancer Man leaves, and First Elder tells Quiet Willy that "you can proceed now". Quiet Willy leaves.
Mulder meets Scully; she says Skinner is the mole, and asks him to say she murdered the man. Mrs Scully and Bill Scully arrive. Mulder meets Bill Scully, who says to leave Scully alone and let her die with dignity. Outside he meets Cancer Man, who congradulates him on breaching the Advanced Research Facility and finding Scully's cure. Mulder says its useless, but he says "on the contrary, it's essential to her survival". They step outside to talk, later Mulder visits the Lone Gunmen. They tap the vial some more, and an Implant microchip comes out. Mulder realizes Scully's cancer devealoped after she removed her Implant; it's a cure.
Kritschgau is brought before the FBI panel including Blevins, Senior Agent, and Skinner. Blevins and Senior Agent question him on giving classified information to Mulder and Scully. Kritschgau tries to talk about the conspiracy but they refuse to hear about it. He says that his son died earlier this morning. He says that he works for DoD but is partially paid by "a Congressional lobbying firm, something called 'Roush'". Skinner asks him what it is, but he's doesn't know. Skinner makes note of it.
Mulder talks to Scully about the Implant; she agrees but Bill is pissed at Mulder. The doctor is uncertain. At first the PET scan shows no improvment on the cancer, and Scully turns to her religious faith.
Cancer Man calls Mulder for a meet to earn his trust; a resteraunt he drives up with an Adult Samantha. Mulder meets Samantha, and they talk for a long time. She says she doesn't remember what happened or wants to; she lived with foster parents until they took her to see her real father one time. It wasn't the father she remembered, "he told me that it had all been a family secret, and that he and Mom hadn't told anyone to protect the family". Her new father was very kind to her, the only person she remembered from before. She meets him now because her father just told her he'd found Mulder and Mulder wanted to see her very badly. Mulder says her father has know where he was for a long time and is lying to him. Samantha says he's the only one who's cared for her. Mulder wants to take her see Mom, but she does't want to. She says she has children and family of her own now and leaves with Cancer Man. Mulder keeps asking how to contact her, but she says she'll think about it.
Cancer Man meets Mulder in the streets, observed by Quiet Willy through an assassin's rifle. Cancer Man offers him the truth about the conspiracy. Mulder says he does know from Kritschgau, but Cancer Man says "he's seen but scant pieces of the whole... he has deceived you with beautiful lies" that there are no aliens. Cancer Man says "quit the FBI, come work for me. I can make your problems go away". Mulder refuses, and promises to kill him if Scully dies. Cancer Man notes he's in trouble with a murder investigation.
First Elder is watching the televised Human Cloning Hearing; the spokesman says it will continue. Skinner appears on the television and talks with a Senator. First Elder angrily calls someone saying "he's gathering information. For who? Our colleague was supposed to have fixed the FBI problem. You will fix it now, do you understand me? Then I will fix it for good".
Mulder meets with Blevins and Senior Agent. They have the forensic reports which say Mulder's gun killed the man. They say Skinner "has been working inside the FBI with a secret agenda. We've accumulated some substantial evidense against him". They suggest that if he testifies against Skinner he'll be exonerated of the murder charge. Mulder refuses.
Mulder is questioned by the FBI panel including Blevins, Senior Agent, and Skinner. Mulder offers to name the FBI mole, and outlines the conspiracy. Skinner asks for a recess but if refused. Senior Agent keeps asking Mulder if he shot Ostelhoff. Mulder names Blevins as the FBI mole. The entire panel is shocked, especially Blevins who storms out of the room. Soon after a nervous Blevins rushes into his office, where Senior Agent is just hanging up the phone. Senior Agent shoots Blevins with a silenced weapon and puts the gun in his hand, it's a suicide.
Cancer Man is standing at his apartment window, looking at the picture of Fox and Samantha. Quiet Willy shoots him with the assassin's rifle from across the street. Cancer Man collaspses, pulling the picture towards him before he passes out.
Skinner tells Mulder that Cancer Man is dead, shot through his window. There's no body, but he lost too much blood to live. He gives him the blood-stained picture of Fox and Samantha. Mulder just guessed the mole was Blevins, but Skinner has learned that "Blevins had been on the payroll for 4 years to a biotechnology company called Roush, which is somehow connected to all this", but the connections are being erased now. Scully's cancer has gone into remission, but they will never know what did it.

Plot Points:

The Syndicate is very interested in a Senate Subcomittee Hearing on Human Cloning, which decides to allow it to continue.
Cancer Man gives Mulder the cure to Scully's cancer: the Implant which was in the vial that Mulder stole from the Pentagon Vault.
Kritschgau and Blevins were paid by ROUSH- a Congressional lobbying firm and biotechnology company.
Cancer Man shows Mulder an Adult Samantha who says Cancer Man is her loving father and she has children. She is afraid to get involved with Mulder or her mother. She says Cancer Man and Mom kept her true father a secret to protect the family.
Cancer Man offers Mulder to quit the FBI and work for him, and learn the truth. Mulder refuses.
When First Elder learns Skinner is investigating ROUSH, he has Quiet Willy assassinate Cancer Man. Too much blood was lost for him to survive, but there was no body.
At the FBI panel hearing, Mulder names Blevins as the FBI mole. Blevins is then killed by Senior Agent.
Scully's cancer has gone into remission because of the Implant and/or a religious miracle.

Analysis:

So when Mulder and Ostelbott had their little shootout, Mulder managed to shoot him in the head! Good shot!
Obviously the Syndicate wants human cloning to be legal because it will make the Hybrid program much easier to carry out if they procure the neccessary supplies and so forth legally.
So Quiet Willy is not a Cancer Man assassin, he seems to work directly under First Elder.
First Elder says they're exposed from what Mulder "may have seen" at the Advanced Resarch Facility. Obviously he didn't see the security camera tapes which Cancer Man saw, because it tracked Mulder's progress at every point! Then again, there didn't seem to be any cameras in the DoD chambers, but we probably just didn't see them.
When First Elder says Quiet Willy can proceed now, this must mean the assassination of Cancer Man. Yet near the end of this episode, he calls a co-conspirator and says he will handle the FBI problem, then First Elder will take care of the matter permenantly (ie kill Cancer Man). But he already ordered the assassination, so perhaps he was confusing his present tense.
It's pretty hilarious that Mulder and the Lone Gunmen didn't notice the Implant when they first opened the vial. They never looked inside with a light? They never tapped it? This is Scully's life here!
Obviously if Cancer Man wanted Mulder to join him, he would have to save Scully's life. This means the Implant would have cured her cancer. Then again, Scully takes a PET scan after getting the Implant inserted and she hasn't improved. Then again, maybe it just takes the Implant a while to get working. There's another possibility; the Implant seems to only freeze the cancer's progress, so when an abductee is first returned she has the makings of the cancer but its progress is frozen. So perhaps the Implant would just have frozen the progress of Scully's cancer, meaning she would live sick for the rest of her life (an incentive for Mulder to work with Cancer Man?). So perhaps it was the religious miracle that caused it go into remission. That's certainly what the episode hints, but the most likely explanation is just that the Implant made the cancer go into remission.
Kritschgau's son just died. Obviously he was killed by the Syndicate for turning against them, cause it would be too big a coincidense if he just happened to die of his sickness that day.
So what is Roush? Kritschgau calls it a Congressional lobbying firm, Skinner later calls it a biotech company. It must be both, but obviously this is the Syndicate in its purest form, its company form.
Obviously this Adult Samantha is an Adult cloned Samantha Hybrid, like the ones in "Colony" and "Endgame". These Hybrids are off working on making more Hybrids somewhere in the nation (like the Adult Kurts in "Memento Mori") so Cancer Man grabbed one, told it the cover story, and sent it in to convince Mulder to join him. It's a good move, because Samantha said she didn't want to be with Mulder anymore so it's a legitimate excuse why Mulder wouldn't get to see if he became a Syndicate man.
So anything and most likely everything that Samantha said is a lie told from Cancer Man. Again he's playing into the theory that he's Mulder's or Samantha's biological father.
This is the end of the Cancer Man cares for Mulder thread. When Cancer Man returns in late Season Five and early Season Six, he is using his biological son Spender to screw over Mulder.
So if Quiet Willy had orders to kill Cancer Man, why didn't he do it when Cancer Man and Mulder were talking on the street? Perhaps he was ordered to do it in his apartment rather than in public for secrecy reasons.
Cancer Man confirms that Kritschgau was an idiot who made up his own theories with what little he knew. He also says that aliens do exist to Mulder, but of course for most of the Fifth Season Mulder doesn't believe in aliens anymore!
Obviously Cancer Man was offering to get Mulder out of the murder investigation if he joined him.
So what would have happened if Mulder agreed to join Cancer Man? Probably exactly what happened to Spender in "Two Fathers" when he did so. He is partnered with a professional assassin and sent to see/kill a Hybrid. So Mulder would have likely become an official Syndicate scout and assassin (rather than an occaisonal unwitting one!).
So what was Skinner doing at the Congress hearing? Most likely asking various Senators what Roush is. Since Skinner is at the Human Cloning hearing, he obviously knows at this point that Roush is also a biotechnology company, as he tells Mulder at the end.
Who is First Elder talking to? It's a co-conspirator, but he talks down to him giving him orders. This means it can't be Well-Manicured Man, but it seems unlikely that it's just another one of the Syndicate Elders. A likely canidate is Senior Agent in the FBI, who we soon learn is also a Sydicate man. He orders whoever to fix the FBI problem; Senior Agent kills Blevins. He calls Cancer Man their colleague; Cancer Man is often seen at the FBI and in "The Pilot" he met with Blevins and Senior Agent.
So Blevins knew that he was in danger of being exposed, so he tried to get Mulder to expose Skinner instead, thus getting him off the hook. Blevins said Skinner had a secret agenda, but it's hard to believe he had any evidense. Is talking to a few senators illegal?
Skinner asked for a recess because he was afraid that Mulder was going to name him as the FBI mole.
Why does Senior Agent suddenly harp on whether Mulder killed Ostelhoff? Doesn't he want to let Mulder name the FBI mole as Skinner, as he said he would do? He must have gotten upset at Mulder outlining the conspiracy to the FBI panel and wanted to shut him up on the matter to protect the Syndicate's secrets.
Presumably Senior Agent will replace Blevins as the Syndicate mole and FBI Section Chief.
So how DOES Cancer Man survive? We never know. He wasn't wearing a bullet-proof vest because there's blood. He lost too much blood to live. A likely explanation is that he got a Pilot or Smith Hybrid to heal his wound, but this healer would have to be in the apartment for them to get there quick enough to save him.
When Cancer Man returns, he seems to have dropped Mulder as his pseudo-son and moved on to his biological son Spender. This must be because of his near-death. While he's on his apartment floor, his blood pumping out of him, staring at a picture of Fox and Samantha, he probably thought it wasn't worth it, he puts his ass on the line to get Mulder to work with him, and he gets shot for it! This must have been the straw that broke the camel's back, after all the hassles Mulder has put him through this must have been it. He rejects going after Mulder and turns to his estranged son instead, which we first see in "The Red and the Black". Need clarification? Skinner or the police finds the Fox & Samantha pic at Cancer Man's so he didn't take it with him when he left. Yet in "Redux" Cancer Man stole this picture from Mulder's apartment and cried about it! See!
Skinner knows where Cancer Man's apartment is here. This must mean its the same one in "Zero Sum" which Skinner visits because he's working for Cancer Man at the time. Now that they have samples of his blood, can't they get his DNA from it? Even if his DNA records have been erased, they now have his DNA for later use.
So was any incriminating evidense found at Cancer Man's apartment?
When Skinner says Blevins has been on the Roush payroll for 4 years, he most likely refers to "The Pilot" when Blevins assigns Scully to Mulder. But as we all know, "The Pilot" took place in 1992 so it is actually 5 years ago!
So Blevins wasn't on the Roush payroll before he assigned Scully to Mulder? It seems surprising that he could be turned so quickly like that!
As an aside here, there's been a long-running rumor that Bill Scully is a Syndicate man. His appearance here certainly supports that, he is very adversarial to Mulder and his quest for aliens.
Scully's cancer is in remission. Presumable it goes away completely cause she's find after this.

UNUSUAL SUSPECTS

The Run Down:

May 1989: John Fitzgerald Byers is a public affairs officer for the Federation Communications Commission. He attends a computer convention in Baltimore where Langly and Frohike are competiting cable bootleggers. Byers notices a woman, Susanne Modeski, and talks to her. She says her little daughter was kidnapped by her psychotic former boyfriend, her only lead is an internet address for "the Arpanet. It's a government network created by the Defense Advanced Research Projects Agency". Byers types in the address, which kicks to the Defense Data Network which is password protected. At Susanne's urging he hacks it, and gets an encrypted file on the 'daughter' Susanne Modeski. He prints it out her. She identifies her psychotic boyfriend as FBI Agent Fox Mulder who appears. Byers enlists Frohike's help to follow Mulder, but Mulder sees them. He tells them he's with the FBI and looking for Susanne.
Military police arrests the man at Byers' computer where he hacked for Susanne. Byers and Frohike enlist Langly to hack the FBI database; Mulder is a normal FBI agent, but they learn about Susanne; she is an employee at the Army Advanced Weapon Facility at White Stone New Mexico. She blew up a lab and killed 4 people. Susanne tells them she was in truth an organic chemist for the Advanced Weapons Facility, until she tried to quit. She devealoped the Ergotimene histamine gas (EH gas), "an aerosolized gas which in small doses caused anxiety paranoia", which the government is going to test on the public here in Baltimore. The printout is proof of the government conspiracy. She says "they want to control every aspect of our lives".
They hack the printout; it says "surprise defection of Dr. Susanne Modeski is a blow to the program but not a fatal one. The time table remains unchanged. First EBO (Engineered Biological Operation) will occur in the Baltimore-Washington area within one week's time. Security risks are being attenuated. Dr. Modeski's team has been processed and plausible deniability constructed", that Susanne is under constant surveillance from "covert electronics" installed by her dentist in '88. They get the location where the EH gas is being stored. Susanne says they killed her team and blamed her for it. Susanne pulls out the tooth her dentist worked on; it has a bug inside. They flush it and agree to help her.
They break into the warehouse and find the gas stored in asthma inhalers. Mulder arrives to arrest the four of them, but he interrupted by two men in trenchcoats who shoot at him. The EH gas containers are shot and Mulder is exposed to the escaping gas. He becomes derlious and strips off his clothes. One of the men is about to execute Mulder but Susanne shoots him first. Severed suited men arrive, led by X. X looks at Mulder and says "sanitize it". The men come in with moving and cleaning equipment. Mulder hallucinates that they are aliens. They remove the EH gas boxes and clean the warehouse. They put the still-living shot man in a body bag. One of the men asks X if they should "bag" Mulder. X looks closely at Mulder's face and says "no one touches this man". Byers shouts to X, asking what gives him the right. X says "no bags", and fires a dry gun at Byer's head then says "behave yourselves". Byers continues to shout about what Susanne said about a government conspiracy being true, about JFK getting assassinated. X says "I heard it was a lone gunman". X leaves with his crew of men and with the evidense.
Police teams storm the warehouse, finding the Lone Gunmen and a derlerious naked Mulder screaming "they're here!". The Lone Gunmen are arrested and questioned by Detective Munch; Mulder is still delerious. Byers tells Munch the whole story. Mulder eventually comes to and clears the Lone Gunmen; they are released. Mulder's stolen car was found at a train station, which is next to a newspaper office. The trio finds Susanne leaving the office; they didn't believe her but she will keep looking for someone who will believe her. A phone booth rings next to them. Susanne flees, saying they'll never be too paranoid and to always search for the truth and tell people about it. Two cars come by, and men grab Susanne. X is in one of the cars.
Mulder meets the trio later; Susanne is still missing but her case has been closed. Mulder asks them what is was all about, he has some wierd ideas in his head now. The Lone Gunmen tell him about the government conspiracy and Susanne.

Plot Points:

Enter Susanne Modeski: an organic chemist for the Army Advanced Weapons Facility who created the hallucinatory EH Gas. When she learned it was to be tested on the public she tried to quit and went into hiding as a fugitive from the FBI. She stopped the testing but got captured by X later.
The Lone Gunmen formed in 1989 because of Susanne Modeski. They also met Mulder at the time, who they befriended. They also met X, who let them see a cleanup operation and told them the JFK assassin was a Lone Gunman, hence their name.
In 1989 Mulder was exposed to the EH gas, which made him certain aliens were on Earth. He was first told about the government conspiracy by the Lone Gunmen.
X first met Mulder in 1989 while Mulder was delirious from the EH gas. X made sure that Mulder wasn't killed there.

Analysis:

Arpanet was created by the DoD's Advanced Research Projects Agency. Is this related to the DoD's Advanced Research Facility which was seen in "Redux", which is in DC?
So this semi-Syndicate military complex is in New Mexico, where we later learn there are many Syndicate complexes in the area.
So what good is this EH gas to the Syndicate? Is it going to be distributed come Colonization time? It doesn't seem very useful in controlling the public, the only useful thing it did was make Mulder certain there are aliens on Earth. Then again, in the sequel "Three of a Kind" we learn that the EH gas' sucessor is a mind control drug, which IS useful!
So what did that tooth bug do? It must have been a microphone not a locator, or the Syndicate would have immeadiately found Susanne. But if they could hear what she hears all the time, they could surely track her down by what people say to her; for example when she orders a plane ticket she must say where she wants to go and she will hear which flight she will take.
The conspirator's report mentioned plausible deniability. Sounds like those Men in Black Cancer Man-wannabes who work security at the Area 51 military base in "Dreamland"/"Dreamland II".
Why does Mulder strip off his clothes? Obviously because he's delerious, but is this normal with derlious people?
The shot but living assassin must have been put in the bodybag to die because he failed to capture Susanne and even got shot. But what about the second assassin? Did he get punished?
So in 1989 X knew that Mulder was not to be killed. This was most likely because of Cancer Man's standing orders not to kill Mulder, but would this order have been in effect in 1989? Mulder wasn't on The X-Files yet so he probably wasn't a concern to the Syndicate and Cancer Man yet. It could be because X was an informant to Mulder and an associate of Deep Throat; Deep Throat said in "Deep Throat" that he had been watching Mulder for some time before coming to him; so perhaps in 1989 Deep Throat was keeping an eye on Mulder, so he told his secret ally X to keep an eye on Mulder as well. X did seem to take a while to recognize Mulder, so obviously he wasn't that familar to him.
While we're on that subject, how could X and Deep Throat be secret allies? X is a top assassin for Cancer Man and Deep Throat was the political DC person. It doesn't seem like they'd be working together often! For that matter, X was an associate of both Deep Throat and Marita Covarrubius. Does this mean that Marita and Deep Throat were allies? These two seemed like they'd work together more.
X spared the lives of the Lone Gunmen, probably because he saw they were truth-seekers and he wants as many out there as possible.
Don't all of X's men think its strange that he doesn't kill the Lone Gunmen and lets them watch the cleanup operation? Won't this action get back to Cancer Man, and what would he think of it? Then again Cancer Man spared the life of Frohike in "Musings of Cancer Man" and Morris in "Dreamland II" treats them as a joke so perhaps there's just a standing order to let them live because they're discrediting truth-seekers by the time of the series, but what about in 1989?
So why does that phone booth ring? Was someone trying to warn Susanne that they were coming to take her, someone like Deep Throat. Or was X calling that booth to spook her into action so she'd run?
So Mulder knows about Susanne. Maybe he'll actually get to meet her in Season Seven.
So apparantly before 1989 Mulder was a pretty normal guy. Then after this case, he suddenly believes in aliens visiting Earth and in government conspiracies to control the public! He soon gets the X-Files after this, around 1991.
Presumably Mulder and the Lone Gunmen became friends after this case.

CHRISTMAS CAROL (part 1 of 2)

The Run Down:

Scully visits her brother Bill's home in San Diego with her mother. Bill's wife Tara is about to give birth. Scully tells her mother how her abduction has left her barren. Scully gets a call from her dead sister Missy who says "she needs you... go to her". Scully traces the hall to the Sim house, where the wife slit her wrists in the bathtub hours ago. The phone is and was off the hook. That night Scully has a dream where she sees Emily Sim, the 3 year old girl of the dead woman, then gets the same phone call from Missy. She visits the Sim house and finds Mr Sim in a meeting with two suited men. He refuses to speak to her, but says the calls didn't come from here.
Scully talks to Kresge, the officer in charge. There was a domestic disturbance call a few weeks before. The wife was taking a new migraine med and was hopped up on it when she killed herself, there were packets of it around her. Scully takes a pic of Emily and finds she is identical to Missy at that age. Emily is adopted, her birth records are sealed. Scully has a dream where as a girl she is taken by Mr Sim to a church, where Mrs Sim is in a casket filled with water and roses, and she opens her eyes.
Scully does an autopsy on Mrs Sim thinking she was murdered. Mr Sim was with Emily at a doctor at the time, he called it in but he would then have to put the phone back off the hook. The meds don't appear in her stomach, only her blood. There is a tiny needle puncture on her ankle; a syringe is found at the Sim house but Emily has a severe form of anemia and requires daily injections.
A blood test finds the DNA of Emily and Missy matches; there is a 60% chance that Missy is Emily's mother. Emily was born in November '94, during that time Missy ran off to the west coast without contacting them. Mrs Scully says she went through the same thing Scully did when her dad died, she would see him in dreams and hear him on the phone.
Kresge finds Mrs Sim has been getting expensive checks from a pharmaceutical firm (Transgen Pharmaceuticals) for the past 18 months. A Dr. Caldron there says Emily is a subject of a clinical test of new gene therapies, she has a rare form of autoimmune hemolytic anemia. Mr Sim brought Emily to his attention, the payments were to quiet Mrs Sim who disagreed. Mrs Sim was going to pull Emily out of the test but Mr Sim countermanded her. The migraine meds were perscribed to Mr Sim. Mr Sim is arrested for murder, and Scully briefly meets Emily and gives her her cross necklace. Mr Sim confesses to being in the house when Mrs Sim killed herself, even though several witnesses put him at the doctor's with Emily at the same time. Scully visits Mr Sim in jail right after he is visited by two men claiming to be his lawyers. He is hanging from sheets, and soon dies.
Scully tries to adopt Emily, but the case worker is reluctant because Scully is always away at work and has never been in a relationship, and Emily is a special needs child. Scully says she's changed her priorities since her cancer, and she's ready to relieve her experience with Emily's sickness. On Christmas day, Scully gets back the DNA test on Emily's blood: Emily is Scully's child!

Plot Points:

Emily Sim, a three year old girl with a strange case of amenia, is Scully's biological child. Her parents were killed.
Emily underwent an experimental gene therapy treatment with Dr Caldron at Transgen Pharmaceuticals at her father's urging. The mother was against it, she was killed. The father confessed to being involved in her death even though he was seen elsewhere at the time, and he was killed by two men claiming to be his lawyers.
Scully was led to Emily by phone calls from her dead sister Missy. Her mother suffered similar things from her dead husband at first.

Analysis:

So after knowing about for like a year, Scully only tells her mother now that she is barren because of her abduction? Surprisingly, Mrs Scully takes this in stride without getting angry about it, yet in "Memento Mori" she practically has a panic attack because Scully didn't immeadiately tell her about her cancer.
We've seen in "Beyond the Sea", "Ascension", and "One Breath" that the Scully women are psychic. Obviously Scully is psychically hearing and seeing Missy from the dead, who is trying to warn her about Emily because she knows how Scully is feeling about not being able to have a child. Mrs Scully suffered the same kind of phone calls from her dead husband as well.
Well these two men who appear with Mr Sim and later kill him are obviously conspirators of some kind. See "Emily" for more!
Mr. Sim appears to be in slightly with the conspirators. Perhaps he knew what he was adopting but his wife didn't. So he takes Emily to Transgen where the conspirators will experiment on her, her wife objects too much so they kill her, then Mr. Sim can't take it and confesses to he's killed.
Emily was born sometime in November 1994. Scully was harvested on October 29, 1994 ("Memento Mori") so that means after the Hybrid fetus is removed from the abductee birth mother, it spends at most a month elsewhere.
Emily's been at Transgen for 18 months. This is December 25 1997, so Emily began treatment around June 1996. This is around the events of "Talitha Cumi"/"Herrevolk".
So just because the migraine meds were perscribed to Mr. Sim, that's grounds to arrest him for murder?!
Mr Sim confesses to being in the house when Mrs. Sim killed herself, does this mean he confessed to murder or what?
So how could Mr. Sim be sighted at another place while he was (possibly) murdering his wife? Because of morphing Hybrids and Pilots!
So is Scully going to quit the FBI in order to mother Emily? She would have to, or else take a deskjob and stop running across the country with Mulder all the time.
So Emily is the Hybrid child birthed to Scully during her abduction by the Syndicate. Thus far we've seen the following Hybrids: Gregors, Adult Samanthas, Smiths, Young Samantha drones, Young Kurt Drones, Adult Kurts, Grey-bodies, now Emily. So apparantly at different places across the country, abducted women are popping these things out in batches. In "Memento Mori", we learned that the batch that Scully was in produces Young Kurt Drones. Yet here she has Emily, who doesn't fit into any categories at all!

EMILY (part 2 of 2)

The Run Down:

Scully recruits Mulder's help who has Frohike hack the California Social Services Adoption database; Emily's surrogate mother is Anna Fugazzi, which means fake. Mulder says her birth records were faked because she wasn't born to a system that keeps records, that she was "a miracle never meant to be". Mulder tells her what he's been holding back from her which they will use against her at the adoption hearing; that genetic experiments were being done, that children were being created for an unknown purpose. At the hearing Mulder tells the Judge about Scully's 4 week abduction and how all her ova were extracted, how a medical exam of Scully would show she hasn't given birth.
Scully gets a blank phone call, and traces it back to the center where Emily is sleeping. Emily is a dehydrated fevered state and there is a patch of green on the back of her neck. They take her to the hospital; there is a cyst on her neck. A nurse does a biopsy, and Mulder realizes the danger too late. The cyst bursts and green blood flows out; the nurse gets infected with the alien retrovirus and collapses. Mulder has the nurse put in an ice bath like Scully did to him in "Endgame" and the nurse survives.
Dr Caldron refuses to transfer her med records because it will expose Transgen's experimental meds and says they are causing Emily harm. Mulder visits Caldron and roughs him up some, accusing him of abducting women and stealing their unborn children. Mulder then follows Caldron who drives to an elderly home where the two suited men are inside. He reports to them that Mulder knows he's involved and asks what he should tell Mulder. One of the men stabs Caldron in the neck with a Glimlet, Caldron bleeds the green blood and collaspes. The two men morph into Caldron. One Caldron leaves in Caldron's car, followed by Mulder.
Emily undergoes an MRI; there is "an autoplastic mass, tumorous infection" growing into the middle of her brain, originating from the cyst at her neck. It is growing rapidly, but unlike cancer it is growing controlled; "these are anaerobic channels following the path of the nervous system. They have the effect of killing the surrounding tissue, depriving it of the oxygen it needs to survive. The origan is in the brain and nervous system". They have her on a levophod drip to keep the blood pressure up and intravenous steroids to bring down the inflammation. Her immune system is too weak for radiation therapy.
The second Caldron goes to the hospital and injects Emily with a green serum. Emily is found turned over when she was facing up before. Scully sees him and gives chase, but he escapes her by morphing into a different person. The injection doesn't seem to hurt Emily at first. Mulder follows the first Caldron to Transgen at the same time; he tells Scully that Caldron was probably trying to treat her, because he wants her alive for his own reasons.
Emily's fever goes down and vital signs are improving, but the growth continues to spread and is necratizing the tissue, shutting down the tissue while it continues to grow. The doctor says Caldron's injection helped, but Scully think it didn't. When Emily is put in an hyberbolic chamber and the air pressure is increased, every vein pops to the surface and she is in great pain.
Mulder visits the elderly home and finds a 71 year old Anna Fugazzi, who asks if he's the new doctor. Mulder reads the list of 8 elderly women to Frohike; they all gave birth to children, including on Sep 25 '94, Mar 18 '86, June 1 '94. All the women are currently on estrogen and pretesterone; hormones that pregnant women have in abdundance and need. They were being treated by Caldron, who have them "beauty sleep" treatments which takes years off their appearance. In this room are 6 women who seem to be in a coma with an IV. In an adjacent room Mulder finds a fridge with 4 containers with two containers each. One is labelled for Dana Scully, 13-10-94. Inside is a living kicking fetus in a flask, and nearby is a box full of green vials. Mulder is about to leave with some green vials but Kresge arrives at puts a gun on Mulder, then Caldron soon arrives. Mulder flees with one vial, telling Kresge to flee and not to shoot Caldron. Caldron throws Kresge with superhuman strength and is about to go after Mulder when Kresge shoots Caldron. Green blood oozes out but Caldron is unaffected. Caldron walks up to Kresge, who collaspses, infected with the alien retrovirus. Caldron morphs into Kresge and goes outside, telling Mulder he has Caldron subdued. Using the distraction Caldron/Kresge flees in Caldron's car.
Emily goes into a coma, and Scully decides to let her die rather than put her through the painful treatments. Mulder doesn't tell Scully about the green vial he recovered. The evidense is being covered up, the elderly women have been transferred and the elderly home 'cleaned up', Transgen didn't know about Caldron's work. Kresge is recovering.
Emily's funeral, the Scully family attends. Tara has given birth to Matthew Scully. Scully says that Emily found her so she could save her, that there is still evidense of what they did. She opens the coffin; inside is only Scully's cross and sand.

Plot Points:

When Emily stopped Caldron's treatments, she became fevered and a green cyst devealoped on her neck. It had green blood and alien retrovirus inside. An autoplastic mass, a tumorous infection, which slowly replaces her nervous system and grows into her brain. It is more ordered than cancer. She went into a coma and Scully let her die rather than put her through a painful treatment.
Scully did not give birth to Emily; Emily's birth mother is an elderly woman, who at an elderly home is given pregnancy hormones and put into a semi-coma at times which restores their appearance. Some of these women have given birth in '86 and '94. Also at this nursery home is a box labelled Dana Scully which has a living alien fetus and green vials.
Emily was being treated by Caldron, a Hybrid, and two morphing Hybrids. They gave her injections of green serum. With Emily turning to the worse, they managed to inject her once which helped her fever and vials but didn't affect the tumor growth.
Emily's body disapeered from her coffin somehow.

Analysis:

Wait, so Mulder didn't tell Scully about what he learned in "Memento Mori". Yet in last episode and here Scully says that she's known for some time that she's barren. If Mulder didn't tell her, then how did she find out? A regular medical exam?
So Scully never gave birth. Presumably this means she never did child birth, because we already know that she was pregnant with a Hybrid child briefly, so this means that the abducted pregnant women have their fetuses surgically removed before giving birth to them, and these fetuses are then put into these elderly women who are given pregnancy hormones while they're in a coma-like state getting 'beauty sleep', then the women give birth to the Hybrid childs who are then put into green liquid tanks as seen in "Colony" and "Memento Mori".
Mulder says outright here that Scully was abducted for 4 weeks. In "Ascension" Scully gets abducted around August 10th. In "Memento Mori" we learn Scully was harvested on October 29th, then she gets returend in Early November in "One Breath". That's about two and a half months!
Scully gets another impossible phone call leading her to a sick Emily; presumably this was Missy from beyond the grave again, but the writers didn't feel like paying the actress for this episode too.
So what is happening to Emily? She devealops a cyst on her neck (in the same place where Hybrids and Pilots are vunerable) which has the green alien retrovirus blood in it. From this cyst a tumor slowly grows, which slowly replaces her nervous system and into her brain as well. So: she is devealoping an alien nervous system, the main node of which is in the base of the neck! That's why Hybrids and Pilots are only vunerable there. However when you stab a Hybrid or Pilot in the neck, the alien retrovirus doesn't come out with the green blood, which means that in this alien nervous system there is no alien retrovirus which is in the rest of the blood. Yet Emily's has the alien retrovirus, probably because her system is just devealoping so the blood is still there, perhaps it is the alien retrovirus in the blood that is causing this growing tumor.
Emily begins to devealop this alien nervous system when her treatment at the hands of the Caldrons stops. This means they were giving her injections to prevent her alien nervous system from devealoping. Obviously they didn't want her to devealop this, but why not? Perhaps because it would expose her a Hybrid, and they are trying to keep this secret. Then again, they seem vested in keeping her alive, suggesting that Emily is a unique Hybrid and that they are studying her.
This begs the question why does Scully's Hybrid child get to be so special? There are two main possibilties, aside from the obvious writing inconsistancies. One, because Scully is psychic and that somehow screwed up the Hybrid fetus devealopment. Two, there was a religious miracle like the one in "Redux II" (maybe), and the connection to "All Souls" (where Scully sees an angel, a demon, and a vision of Emily!).
So what was Caldron, and what were the two suited morphing men? Was Caldron an inferior breed compared to the two men, and that's why they killed him for failure? Probably. Caldron was probably just a regular Hybrid who was working on the Hybrid babies like the Kurts in "Memento Mori", and the two morphers seem to be enforcers like the Pilots. But in the grand scheme of things, the Syndicate would never call in one let alone two Pilots on so inconsequential a matter, so the two suited men must be Higher Hybrids like the Jeremiah Smiths who can morph and heal. So there must many many different forms of Hybrids, not just five faces or so, perhaps each local abduction center (like the one in "Memento Mori") generates a different type of Hybrid. For example, the "Memento Mori" center made Young Drone Kurts, and the "Redux" center makes Grey corpses.
So there's Drone Hybrids (no language), regular Hybrids, and Higher Hybrids (who can morph and heal), and their alien genes come from the Pilots, who are the strongest kind of alien.
Once again we see Hybrids playing the role of custodian to the newly hatched Hybrids, as in "Memento Mori".
An autoplastic mass is a mass which repairs lesions with tissue from the same body or is related to this repair. So in other words, this autoplastic mass in Emily's neck is slowly replacing her immune system with similar tissue!
Anaerobic channels mean they live or are active in the absence of free oxygen. These channels follow the nervous system, depriving the surrounding tissue of oxygen and thus killing it. So from the cyst, there comes these 'channels' of tissue that doesn't need oxygen to work, which follow the nervous system, slowly killing it and the tissue around it. So it's clearing up the space for a larger alien nervous system, which does not require oxygen to survive. This explains why the back of the neck does not carry the alien retrovirus; in the alien nervous system (of which the hub is in the neck) there is no blood, no oxygen being carried so there's no alien retrovirus. This also hints to how the experimental Hybrids in "The Erlenmeyer Flask" can breathe underwater, perhaps they don't need oxygen or they at least don't need as much of it.
So how in the hell does Scully have Emily? We saw that she was taken to the Lombard Facility during her abduction, and since they produce Young Drone Kurts, she should have produced a Young Drone Kurt. As the Adult Kurts say, "they are our mothers". Yet NOW, Scully pumped out an Emily! Is Emily a regular model, in other words are there other Emilys out there? They seem to be pretty useless; they're too young to be useful as an agrarian workforce ("Herrevolk"). So maybe Emily really WAS a screw-up!
So while one Caldron II went to give Emily a shot, the other Caldron II drove back to Transgen to draw away Mulder.
So these regular green injections kept Emily from devealoping her alien nervous system, yet when Caldron II sneaks an injection to her when she's sick, it doesn't affect the alien nervous system but does help her fever and vitals. Most likely, it was just too little too late to stop the nervous system devealopment.
As for Emily's vains popping out when she put in a hyperbolic chamber, that's harder to say on. A hyberbolic chamber fills with a high pressure purer oxygen content. So here's a far-out theory: Emily has such incredible high blood pressure that when the pressure increased in the chamber, the difference in pressures caused Emily's veins to pop out.
Is it really necessary to put the Hybrid fetuses in these elderly women?! It seems needlessly complicated!
So this whacked out elderly pregnancy thing has run at least since 1986.
Those elderly women currently pregnant seemed to be in a coma, just like the abducted pregnant women in "Redux". But the doctors call it beauty sleep; don't these women get suspicious when they're unconscious for several weeks or days?!
Now Anna said that this beauty sleep takes years off her appearance. How does this do it? Is it just from the hormone meds? Or does it involve carrying a Hybrid fetus?
The abducted women get cancer from their abduction if they remove their Implant. Do these elderly women have an Implant, and if they remove them will they get cancer? Most likely not, since this cancer seems to come from the high amplification radiation which causes the superovulation in the abducted women.
This elderly home has the WORST security a Syndicate complex has ever had! Not a single freakin' guard or security device, and it holds some vitally important evidense!
So Scully has an unborn fetus sitting in here. Anna said that Caldron was supposed to come today for her next 'beauty sleep'. So that fetus was about to go in Anna to give birth to it, but Mulder interrupted it! This means that the same old women will have the babies of the same abducted women.
How can Scully have a second baby if she's barren? The Syndicate took all her ova, but only used ONE to create Emily. So from one abducted women they can get almost a thousand viable eggs, thus a thousand Hybrids! If this is the case though, why are the Allentown women abducted several times? Sure, even though they're barren if the conspirators put a fertelized egg in her and gave her pregnancy hormones they could still have the baby. Even worse, this fertalized egg could be put in any viable women and she could carry it! This means the Syndicate could get a thousand Hybrids from one woman, 100,000 from one hundred women, a million from a thousand women, a billion from a million women! It seems that the Syndicate has abducted around a quarter billion women by now, so that means they could have a quarter trillion Hybrids!
Of course they are most limited by the amount of alien sperm they can get.
Shouldn't there be more security at this facility... AT LOT MORE?
So a Hybrid (human looking) fetus can get sustinence from that green liquid, it doesn't need oxygen. Maybe those green vials were not for Emily, but 'food' for the fetus.
There were a total of 8 fetus holders there, but there were 12 women. Which means that those other 4 just already have fetuses in them.
Mulder should have told Kresge that if he shot Caldron he would infected with a virus, maybe then Kresge wouldn't have shot him!
Two people got infected with the alien retrovirus; isn't this conclusive proof of alien existance? That alien retrovirus was a huge piece of evidense back in "The Ernlenmeyer Flask", why is it worthless now?
So Kresge shot Caldron, but Caldron wasn't affected. Caldron bled green blood which almost killed Kresge. Caldron threw Kresge with superhuman strength. Did Kresge testify to this effect? Does he now believe in aliens? Isn't this a supporting testimony to Mulder? But wait, the episode's over so all the evidense they see and learn conveinently disapeers and any legal trouble they get into conveinently goes away!
Mulder sees Kresge shoot Caldron and get infected. Yet when Kresge appears outside, Mulder never even considers that it isn't Kresge! What the hell was he thinking?!
Now Mulder has a vial of an alien green liquid, which might be alien blood. Does he ever have this analyzed?! Isn't this absolute proof of alien existance?! But wait, the episode's over so it conveinently goes away!
Even if the elderly women have been transfered, don't they still have those Hybrid babies inside?! But wait, the episode's over!
If Caldron worked at Transgen without them knowing, how could Caldron call in security guards to haul away Mulder earlier? Transgen must be a Syndicate company so they just say that.
Scully thought that Emily's body was in the coffin, that why she said there's still evidense. Since there was sand in the coffin, it means someone stole the body and put sand in to fake the weight of the body. Obviously it was the Syndicate who stole the body. Here's an interesting question: if a Hybrid (like Emily) dies but not from a Glimlet to the neck, what happens to the body? It must not dissolve into green gas like when they're killed with a Glimlet, so perhaps they just die and wither like the pre'73 Hybrid corpses seen in "The Pilot" and "Anasazi".
It was very nice of the Syndicate cleanup team to leave Scully's Cross in the coffin!

KILL SWITCH

Plot Points:

The Department of Defense has orbiting satellites ("Warbird grade orbital weapons platform") which shoot a powerful lazer with optical tracking systems that can read newspaper headlines. Scully says these Star Wars satellites were never built, the tech isn't there.

Analysis:

These DoD lazer satellites would be the perfect weapon to use against the Colonists when they come to Colonize the planet in 2015! Sure, they probably wouldn't be able to hit the UFOs when they're moving, but as we see in "Patient X", when Colonization time comes... the abductees will be Drawn to a Lighthouse, where a Colonist UFO will be waiting for them, hovering there. Surely the Colonists are not aware of these, so if the Syndicate decided to resist the Colonization, they could blow away the first wave of UFOs. Of course, that would only be a tempoary situation because the next wave of invading UFOs would just toast the Warbird satellites.
On the other hand, the Syndicate could use it to take out any human military resistance against the Colonization.

PATIENT X (part 1 of 2)

The Run Down:

Mulder narrates... in earlier times man said that the heavens were the realm of powerful warring gods who controlled not only the heavens but the past and future of man, for which great monuments would be created on Earth. Now man has new religions of monotheism and science, but still they wait for a sign, a revelation, from the heavens. Our destiny is written in the stars.
Kazakhstna, Russia: a UFO lands from orbit. Two boys see it and say "they're here" and go to tell the others. They find the others; twenty cars in a clearing burning away with people inside. One boy runs into a Faceless Rebel, who looks like a Pilot but with no openings on his face. The other body Dmitri escapes but hears his friend's screams.
The next morning a UN convoy arrives, led by Marita Covarrubius. They begin putting out the fires and inspecting the bodies. Dmitri is captured by Krychek, who is leading a group of Russian agents. Dmitri tells Krychek he saw what happened, and Krychek says "too bad for you". The UN troops find the bodies have their flesh cooked right through to the bone. Krychek accuses Marita of corrupting the scene. Marita spouts UN code saying she is "a Special Representative to the Secretary General" but Krychek says "your authority isn't recognized here. Only your lies. This is a mission of fear. Yours and the men you work for. You go back and you tell them what you've seen here, what you've found. I know who you are and who you work for. Tell them it's all going to hell". Marita sees Dmitri and asks if he knows what happened, Krychek doesn't answer.
Mulder attends a UFO conference. Cassandra Spender, a wheel chair bound repeated abductee, says (on a film) that "during my last several abductions I have experienced no fear whatsoever. And it was the absence of fear that allowed me to communicate with them and them with me. They've told me that I am an apostle, here to spread the word of the dawning of a new age of supernatural enlightenment". The speakers call her Patient X and say that she thinks the abductions and experiments show man not be breeding cows to them but subjects as they are subjects of God. "And that there are sites- what she calls lighthouses- around which will be great activity". Mulder spouts the Kritschgau retoric, that it's all just an government military conspiracy to hide their sins with fake aliens, that all these people are believing a lie. Mulder meets Dr Werber (who gave him regression hypnosis to remember Samantha's abduction) who he hasn't seen in 5 years, Mulder says he doesn't believe those memories anymore. Cassandra is also Werber's patient.
Tunguska Gulag, Russia: Krychek has learned the truth from Dmitri by beating it out of him. He orders the Doctor to begin, but the Doctor says "but he is just a boy. We do our experiments only on the criminal. I have orders". Krychek forces the Doctor to do it, and pays off the Guard to forget what he saw. Krychek leaves, stealing one of the amber serums on the Doctor's tray. Dmitri asks the Doctor if he's going to kill him. The Doctor says "no, we are doing a test". Dmitri is infected with Black Cancer, which moves as one puddle sliding into his mouth and nose. Russian Smoking Man is angry talking with Guard, saying "why was I not informed of this?". Guard says "Krychek was given orders". Russian Smoking Man asks where the boy was captured, Guard says "I was told there was a site. People were burned alive". Russian Smoking Man asks what the boy knows, Guard says "I don't know. Only Krychek knows. He interrogated him, beat him. Then he ordered the test". They find the Doctor hanging in a cell, which greatly angers Russian Smoking Man. Krychek is on a Russia freighter, and pours some water on Dmitri's face, saying "I'm going to take good care of you". Dmitri's eyes, nose, mouth, and ears have been sewn shut.
Werber introduces Mulder to Cassandra at the hospital. Cassandra says he's her hero, when she read about how he helped Duane Barry 3 years ago it convinced her to finally seek help with Werber. "I have been a multiple abductee for over thirty years" Mulder suggests that she checks herself out and starting living her life. Werber says "Cassandra is experiencing the sensation that she's about to be called". Cassandra says "now is a time of war and stress among the alien nations. The different races, they're in unheaval. I will be summoned to a place, just like Duane Barry. I'm sure the government's involved. They don't want us to know about it all... I have been through the terror and the tests more times than I can count. I have had an unborn fetus taken from me. But they're not here for the reasons that you might think. They're here to deliver a message. Except, something has gone wrong. There are other forces at work. They're going to be calling me. I can feel it". Mulder needs to know about because he's the only one that can do something about it. Mulder refuses and leaves.
Special Agent Jeffery Spender approaches Scully to get Mulder to stop bothering his mother, Cassandra Spender. He says she's demented and he doesn't want it affecting his career. Scully agrees.
Marita reports to Well-Manicured Man and the Syndicate Elders at their NYC Office. Quiet Willy is there. There were 41 bodies "all burned beyond recognition. The result of some kind of intense biochemical reaction, none of the UN medics have ever seen, not in the Gulf or on any battlefield. The corpses were literally carbonized from the heat". 3rd Elder asks "a new weapon being tested?", 1st Elder says "there's no intelligence on that". At least 2 Implants were found in the bodies; Well-Manicured Man asserts they all had them, "that what was taking place was a staging for a group abduction". 3rd Elder doesn't know what that is. Well-Manicured Man says "in the final phases before it begins, there will most likely be assemblies". 3rd Elder says "we're years away from that". 1st Elder says "if we're to believe their timetable". Well-Manicured Man says "unless it's already begun". 3rd Elder says "we're 15 years away!". Marita asserts it wasn't planned by Russia, "I think something, or someone, set in this in motion. An act of war. Against us and our plans". She says Krychek was there with Russian soldiers, "he was there, probably acting on the same data we got. Whether he had any direct involvement in what happened, he knows what caused it" from a boy who saw it. 1st Elder asks what Krychek wants, and 3rd Elder asks how they find out. Just then the phone rings. Well-Manicured Man answered; it's Krychek, who says in New York City. Well-Manicured Man asks what he wants; Krychek says "you've been working on a Vaccine. Against the Black Oil". Well-Manicured Man says "unsuccessfully, you know". Krychek says there must have been progress while he was gone, Well-Manicured Man says "our research continues". Krychek wants it all in exchange for the boy, "because without what he knows, you're not going to need any Vaccine".
Scully tells Mulder about Spender's wish, and learns that Cassandra was abducted from Skyland Mountain too and has an Implant. Scully visits Cassandra, who is idly drawing a constellation. Cassandra recognizes Scully from somewhere, and says "you're feeling it too aren't you?", she motions to the back of the neck, "You wake up at night knowing you need to be somewhere, but you don't know where it is". Scully warns Cassandra not to remove her Implant, it will make her very ill. Cassandra would never do that, "I want to go, wherever it is. They have so much to teach us... they are great healers. Maybe that's why you were chosen".
Skyland Mountain: a large group of confused people feel drawn there and go. A late comer finds many cars stopped, and sees a man being chased by a Faceless Rebel, who is holding a large metal stick, a Lighter. When he pokes the man with it, he bursts into flames. The next morning Mulder and Scully arrive where there is a large police investigation. All were killed, most in a wooded clearing. Scully suspects the connection to her abduction, but Mulder refuses to believe it.
Marita, Well-Manicured Man, and the Syndicate Elders watch the Skyland Mountain on tv. Marita says it is identical to Kakakhstan. 2nd Elder protests that "this is our own backyard!". 1st Elder says "this is no good. I don't like being kept in the dark on this". Well-Manicured Man says "someone's going to great lengths to sabotage our work". 2nd Elder asks who, he says "one way or another, we'd better find out before it's determined we're unable to handle this ourselves, to put a stop to it, before the Colonists intervene". Quiet Willy stands and leaves.
Mulder and Scully visit Cassandra; all the Skyland victims were old friends of hers from a long time ago, "this is not supposed to be happening". Spender arrives and protests Mulder being there but Cassandra called them over. Spender says Cassandra and the Skyland victims were in "the same ridiculous cult she used to be in, a UFO cult believd they were going to be carried to immortality in some kind of flying motherwheel". Mulder apologizes and leaves. Quiet Willy arrives.
On the docked Russian freighter, Krychek is surprized to find Marita who says "you think you can pull this off, don't you?". Krychek grabs her and they passionately kiss. Krychek says "they give me what I want, I'm going to rule the world!". Marita says "we've got them on our knees, Alex". They go off to have sex, leaving Dmitri's room unlocked. Later Krychek returns to find Dmitri gone from his cell on the freighter, and an armed Well-Manicured Man waiting for him, who asks where the boy is.
Scully is sleeping when she suddenly wakes. Outside is the constellation that Cassandra drew earlier. She feels her neck.
Mulder tells Scully about Skyland; at least 3 Implants were found in the victims. These victims were not in cults in MUFON groups and being treated by a doctor over the past few months for a "major depressive disorder characterized by periods of sustained anxiety and paranoia. Patient believes he will be contacted or called to an undisclosed place where he will be abducted". Mulder asserts the Implants are used by the government as a "tracking system using military app satellite technology to monitor test subjects, or to stage what people might otherwise believe these are alien abductions". Scully says he shouldn't rule out what Cassandra is saying.
Marita calls Mulder in his office from a phone booth, asking if its a secure channel. Mulder says yes. She tells him a similar thing happened in Kazakhstan and she has with her someone who knows what happened. Dmitri is sitting the car, pulling out the stitches in his eyes. She gives her location, but then Dmitri appears outside the phone booth with Black Cancer running from his eyes. She doesn't have time to scream, and drops the phone. Mulder drives out there, and only finds the phone booth with the oily residue on the glass.
Scully disapeers, and Cassandra disapeears. Mulder calls for Scully at Cassandra's hospital and gets Spender instead.
Ruskin Dam, Pennsylvania at night; there is a small bridge running over a river. Hundreds of people stand on the bridge, including Scully, Dmitri (with his eyes and mouth unsewn), and Cassandra whose wheelchair is being pushed by Quiet Willy. A blue light approaches them slowly, then when it gets near them it switches on great white lights. It is the underside of a triangular UFO, and continues to coast along. Scully recognizes Cassandra but not Quiet Willy. Just then, a man appears burning and screaming. Two Faceless Rebels have appeared at the end of the bridge, holding their Lighters and calmly approaching the group.

Plot Points:

Enter the Faceless Rebels: Pilots with sealed faces who carry Lighters, which create an instananeous biochemical reaaction which burns people to the bone. They are executing Lighthouse gatherings of abductees.
Enter the Lighthouses: abductees will feel a drawing from their Implants, which forces them to go to a Lighthouse, where a Colonist UFO will arrive to meet them. This is supposed to happen in the final phases before Colonization. Second Elder didn't know about this.
The Faceless Rebels first strike in Russia, where Krychek finds a survivor and infects with Black Cancer and sews up his face, then takes him to America with the Russian Vaccine. He wants a deal with the Syndicate for their research on the Vaccine.
Krychek and Marita Covarrubius are secret lovers and allies, but she stole the Russian survivor from him and left him to Well-Manicured Man. Marita became infected with the Black Cancer from the survivor.
By sealing your face, it prevents the Black Oil/Cancer from getting in or out.
Enter Cassandra Spender: a crippled repeated abductee for over 30 years, she says the aliens are great healers and bring enlightenment. She was abducted at Skyland Mountain and recognizes Scully.
Enter Jeffery Spender: an FBI agent who is the ashamed son of Cassandra Spender.
According to Cassandra, now is a time of war and stress among the alien nations.
The Colonists told the Syndicate that Colonization would occur 15 years from now.
When it is determined the Syndicate can't handle a problem, the Colonists intervene. The Syndicate fears their intervention.
The Faceless Rebels strike again in America after Skyland Mountain, where Scully and Cassandra are.

Analysis:

Mulder's opening narration gives some thematic foreshadowing to future revelations. He says these gods from the heavens were responisble for the past and future of Man; we learn in "The Beginning" and "Biogenesis" that the Colonists most likely created human existance millions of years ago. He says great monuments would be created on Earth; in "Biogenesis" we see a great Artifact buried in the African West Coast, or perhaps this just refers to Colonization itself.
The Faceless Rebels appear to have had their facial orafices carefully sewn shut, in the next episode they say by self-mutilation. This means that the Faceless Rebels may look like Pilots, but they cannot morph. If they could morph, then they could just create their face with no holes in it! Yet in their next appearance in "Two Fathers"/"One Son", they can morph! So why would they bother to mutilate their faces if they could just morph the changes?
In "Herrenvolk" Marita said she was an assistant to an SRSG. But here she says she's an SRSG! She must have promoted!
Krychek says Marita coming here is a mission of fear. What does this mean? That by coming here Marita is spreading fear to Russia? Unlikely. It more likely means that the Syndicate is afraid of what happened and is desperate to find out.
So what's up with this Krychek-Marita thing? In the opening scene they seem not to know each other personally, though Krychek recognizes that she is from the Syndicate. In their next scene, they're passionate lovers. Obviously this wasn't a spur of the moment thing, they have been secret lover and allies for some time. That's how Krychek knows to call right as Marita tells the Syndicate that Krychek knows what's going on. So in that Russia scene they must have been faking it for the sake of their guards.
So for the past 30 or so years, Cassandra has been terrified during her abductions and never learned anything from them. But in the last few times, she wasn't afraid and she was able to telepathically communicate with her abductors, who told her they were bringing healing and spiritual enlightment. Now, in "Two Fathers"/"One Son" we learn that Cassandra is just another Syndicate abductee, but obviously she must be abducted by the Colonists sometimes. Why does she get this special treatment? Because she is one of the 'children' the Syndicate Elders gave to the Colonists as part of their deal. Obviously she couldn't telepathically communicate with Syndicate scientists, but then again she could do so with Higher Hybrids (like Jeremiah Smith and the ones in "Emily"), and we've seen that these people work for the Syndicate.
The fact that Marita could communicate telepathically with her abductors shows that she's getting Hybrid powers, as we learn about in "Two Fathers"/"One Son".
Obviously whoever talked to Cassandra told her a lie about the Colonists being here to spread peace, so she doesn't blab about their true purpose of Colonization and alert humanity. Then in "Two Fathers" she learns the truth, presumably because with her increasing Hybrid abilities she was able to read the minds of her abductors and learn the truth.
When Mulder says he hasn't seen Werber in 5 years, he probably means 6 years since as we all know those kooky writers love to forget "The Pilot" took place in 1992, a year before Season One! Then again, we know Mulder's regression hypnosis (when he first met Werber) took place in 1989 which is 9 years ago.
The Russian Doctor says they only do the Black Cancer Vaccine test on the criminal. Obviously he was misinformed, because in "Terma" we learn that the geologist who first found the Black Cancer was put in there.
Why oh why did Krychek betray his friends in the Russian Syndicate? In "Terma" we learned that he was a very high ranking member in the Russian Syndicate, so he's really shooting himself in the foot here! Then again in "Piper Maru" Krychek was selling US secrets to the highest bidder in Hong Kong, rather than taking them all to Russia...
So by sewing shut the mouth, eyes, and nose of Dmitri Krychek thinks he can force the Black Cancer to stay in Dmitri. So he had Dmitri injected with the Russian Vaccine, then infected with the Black Cancer. Obviously there was a time laspse before the Black Cancer was forced out, time enough for someone to run in there and sew shut Dmitri's facial oraficies. Thus, the Black Cancer is not infecting him (so he's not in a coma) it's kinda stuck in his skin trying to escape his body but is stuck by the stitches. Amazingly, those stitches keep the Black Oil in even though in "Piper Maru" and "Tunguska" they get through heavy diving suits and Hazmat Suits!
Obviously Dmitri was not breathing, or else the Black Cancer would escape. So when a person is infected with the Black Cancer they do not require oxygen. This explains how the WWII pilot in "Piper Maru" could survive trapped in an airplane cockpit underwater for some 50 years! So the Black Cancer somehow supplies oxygen to its host, or removes the need for it. This is connected to "Emily", where Emily's growing alien nervous system was depriving her body of oxygen because it didn't oxygen to work.
So here's the theory: when a human is infected with the Black Oil or Black Cancer, it makes the host body into one big anaerobic channel; it makes the body function without oxygen but somehow altering the state of the body. But if the Black Cancer/Oil leaves the host, the host body can go back to needing to oxygen once it leaves. Perhaps THIS is why Mulder got telepathy from the Artifact's cosmic radiation in "Biogenesis" after his exposure to Black Cancer in "Tunguska".
Why does Krychek pour water on the boy's mouth? Obviously water can't get in there, because if it could then the Black Cancer would be able to get out the same way.
Cassandra has been abducted for over 30 years. 1998 - 30 = 1968. Hold a second! ; Cassandra was handed over to the Colonists in 1973, as we learn in "Two Fathers"/"One Son", and there they say the abductions must have been going on for only 25 years (1973). So maybe by some amazing circumstance, Cassandra was abducted by aliens prior to their alliance with the Colonists! Or maybe she was abducted by the pre-collaboration Syndicate!
Cassandra says now is a time of war and stress among the alien nations. She most likely refers to the Civil War between the Colonists and the Faceless Rebels. There's a smaller chance she refers to the ongoing war between the Colonists and the Whiteout/Willowy Grey aliens. But she must have learned about this from her abductors, why would they tell her this?
Cassandra says she's had an unborn fetus taken from her. Does she mean her abduction, or did she have a baby normally and it was stolen by her abductors cause she made the mistake of already being pregnant when she was abducted. Then again, we learn in "Two Fathers"/"One Son" that Cassandra is part of the 'make a perfect Hybrid' program and the 'give the aliens your children for the deal' program. So it's unlikely they ALSO use her to produce Hybrid babies.
Let's take a moment to look at these abducted women and Hybrid babies: the first time they're abducted, all their ova are stolen. Then the ova is artificially inseminated with alien sperm and put back in the women for a brief amount of time, then the fetus is taken out and put in an old women, who gives birth to it. Yet these women are abducted several times, why? Even though they are barren, if they put a fertilized egg in her and give her pregnancy hormones, she can carry the baby, and carry the baby, and carry the baby...
Once again First Elder acts an intelligence agent, this time on the Russians having a new weapon to test.
Aside from it giving an excuse for Well-Manicured Man to explain things to the viewer, why is it that Second Elder doesn't know these things like Lighthouses but he knows when Colonization will happen?
So these Lighthouses are supposed to occur just before Colonization. All the abductees are drawn to one spot, where a Colonist UFO will appear and do something. Do what? Perhaps it will infect them with Black Oil, creating all those abductees into a slave race? But wait, in The Movie we learn that's not what happens! Perhaps that after the Syndicate creates the Perfect Hybrid ("One Son"), these abductees will be given the Hybrid gene (which will also be given to the Syndicate and their families) and will then function as a slave race in addition to their many Hybrid children.
Colonization will happen in 15 years: 1998 + 15 = 2013!
So at some point the Colonists gave a complicated timetable to the Syndicate, which said that Colonization will come in 2013. Yet in "One Son", Cancer Man says the moment they make a Perfect Hybrid Colonization will happen, and since that happens to Cassandra in 1999 the Colonization will happen in 1999. Whatever happened to the Colonists' timetable. Perhaps it was a projection, that at the current rate of research the Syndicate would produce a Perfect Hybrid in 2013 and then Colonization would begin.
Why does Krychek want the American working Vaccine? His Russian Vaccine works and the American one doesn't! Obviously he doesn't intend to return to Russia with it as a counterespionage operation, because he killed that Russian Doctor and pissed off Russian Smoking Man!
Wow, isn't it a COINCIDENSE that Cassandra just happens to get abducted at Skyland Mountain just like Scully, and that Cassandra just happened to get abducted along with Scully! Funny, because Scully and the Allentown women never mentioned another woman being there! Besides, these things are done geographically, so it was just a huge coincidense that Cassandra lives near Skyland? Besides, Cassandra is likely not part of the Hybrid baby program, so why would she even be with Scully and the Allentown women?
This is the first episode where the Colonists get named the Colonists.
So these Faceless Rebels seal their face so they don't get infected with Black Oil. Yet in "Tunguska" and in The Movie, we see the Black Cancer/Oil infect people through the leg, through the skin! So presumably a Pilot has tougher skin which the Black Cancer/Oil can't get through, and presumably it can't escape through here because it's in the face.
So now Quiet Willy is acting as the Syndicate assassin. They order him to stop the situation; he does this by grabbing Cassandra, thus using her learn where the Faceless Rebels will strike next. So why didn't he have a whole legion of Syndicate assassins with him, and maybe some Syndicate UFOs running overhead for support if he's going to attack and stop these massacres! He seems to think that just with his gun (and no gas mask!) he can stop them!
So Cassandra used to be in a UFO cult with all the people at Skyland. Maybe she felt the calling but couldn't get out of the hospital by herself, so she was supposed to go the Skyland Lighthouse.
So this UFO cult thought they'd gain immortality in a flying motherwheel. Was this flying motherwheel the Colonist Mothership seen at the end of The Movie, which was storing abducted people infected with Black Oil?
Krychek says he's going to rule the world, which seems to come from getting the American Vaccine which doesn't even work. What the hell does this mean? By next episode he's a loyal Syndicate man again, working with former enemies to save the planet. His line about ruling the world doesn't make any sense!
How did Well-Manicured Man know where Krychek was? He probably just tracked as Russian freighters that recently arrived in New York City, rather than get any information from Marita on it because it would make her look suspicious.
So Marita betrayed Krychek, hoping to get Dmitri to Mulder so he would learn about the strikes firsthand and whatever's causing them. Obviously she hasn't been following him closely because now he doesn't believe in aliens!
So abductees who are being drawn to Lighthouses have been feeling depression for the past few months. Has SCULLY been feeling depressed for the past few months? She hasn't seemed to be! She has an Implant! Why not! She's had that Implant in for around six months by now!
Mulder considers his office phone secure.
Even if Mulder's phone is secure, if Marita is calling from a phone booth isn't the call unsecure?
That Black Cancer seemed pretty dead, just plopping out of Dmitri (because it had been hurt by the Vaccine) yet it still had enough strength to go through the glass and infect Marita! This is funny because in "Terma" when people die and the Black Cancer comes out it seems to die quickly.
Since Black Cancer is NOT sentient, why did it attack Marita? Probably because Dmitri kind of threw it at her, and it just mindless went into the nearest body. This means that when an infected human is given the Russian Vaccine, the Black Cancer doesn't die (like when the host is killed by poisoning) it just gets hurt and runs away. So that means the Tunguska Gulag doesn't need to replenish it's Black Cancer supply, it just uses the same amount over and over again.
Obviously the Syndicate traced that call, sent a man by who picked up Marita (but Dmitri was already gone) before Mulder got there.
Notice that there are just as many male abductees as female abductees. Since the women are taken to make Hybrid babies, the men must be taken only for whatever purpose the Lighthouse serves.
So the Faceless Rebels have triangular UFOs identical to the Syndicate UFOs and Colonist UFOs.
Why don't the abductees jump off the bridge into the river? It isn't that high up! Isn't the distant risk of freezing to death better than being definitly burned to death?

THE RED AND THE BLACK (part 2 of 2)

The Run Down:

In an isolated cabin in the Canadian moutains, someone writes a letter: "Dear Son, I hope this letter finds you well. I get reports of you from time to time. I know these letters come as a surprise. You must wonder about me. I remind myself of a Navajo story. Twin war gods come to their father, seeking magic and weapons to eliminate the monsters of the world. My hope is the same for you, and that we might reconcile the differences between us. Your Loving Father, (blank)". A boy arrives to mail it to the FBI.
Medical officials arrive at Ruskin Dam, where there are over 50 burned bodies including Quiet Willy and Dmitri. Scully and about 50 other survivors were found huddled in the woods with minor burns "but her fluids and electrolytes were abnormally depleted. She's in vasogenic shock". Mulder, Skinner, and Spender arrive. Cassandra is missing.
At a hospital, Marita is comatose with Black Cancer running through her eyes. A Syndicate doctor says "it's not a question of dosage, we've administered 3 intramuscular injections over the past 24 hours" since she was found by the roadside, to no effect. Well-Manicured Man is there, along with ten Syndicate Elders.
Well-Manicured Man visits Krychek, who is chained to Dmitri's room on the Russian frieghter. He says the freighter will leave for Russia tomorrow, "I gather there'll be quite an enthusiastic homecoming". Krychek asks if he has the boy. Well-Manicured Man says Marita took him, "your alliance with her was as misguided as ours, but it appears she was unaware of the consequences of her deception. You were clever. Infect the boy to ensure infection of anyone who tried to learn what he knows, who would cheat you". He says the boy was killed in another massacre. Krychek says he'll have to deal with him know, only he knows the truth. Well-Manicured Man says "if the the boy was your trump card why infect him unless you could also cure him with a Vaccine devealoped by the Russians? One that works. It would mean that the resistance to the alien Colonists is possible". Krychek says "you're dreaming. You need what I know!". Well-Manicured Man demands the Vaccine. Krychek doesn't want to give him the means to save Marita after what she did, but Well-Manicured Man said its the means to save himself.
Wiekamp Air Force Base, West Virginia: a triangular UFO crashes into a field. A Faceless Rebel drags out the bodies of two of his compatriots, as Military Police arrives and surrounds him.
Scully awakens with low blood pressure, and no memory of Ruskin Dam at all. None of the other survivors remember either. Mulder asserts the truth about everything is in the Implant, it drew her to Ruskin Damn than erased her memory of it, "as part of a secret military project to devealop a biochemical weapon, to monitor your immunity, or to destroy you... if the truth were exposed".
Well-Manicured Man shows pics of the Faceless Rebel to the Syndicate Elders at the hospital. 1st Elder says "the facial scarrings appear to be self-mutilation done as protection". 2nd Elder asks "protection against what?". 1st Elder says "infection by Black Oil. He was the lone survivor of a crashed spacecraft at a military base in West Virginia". Second Elder says "what the hell is he?". Well-Manicured Man says "an alien rebel. This is what the boy saw in Russia, the last face the dead saw at Skyland mountain, and most surely who killed our man at the dam in Pennsylvania. He's a resistance fighter against the alien Colonists. This is what Krychek knew- that a war had begun". 1st Elder says "what good was that knowledge? Without the Vaccine against the Black Oil, no one can survive". Well-Manicured Man says "we have a Vaccine, devealoped by the Russians, stolen by Krychek, given to me. Do you see what this means? Resistance is possible. We have the weapons and the magic in hand". 1st Elder says "we don't know the Vaccine works". Well-Manicured Man says "it will. And if it doesn't, we have a new alliance to be made". 1st Elder says "side with the resistance?!", 2nd Elder says "suicide". 1st Elder says "they'll squash us as they do them. We must turn the rebel over". Well-Manicured Man says "but first, wait till we know the Vaccine works". Marita is injected with the Vaccine.
Mulder takes Scully to Dr. Werber where using hypnotic regression she remembers what happened at Ruskin Dam: the UFO coasts over the bridge, briefly shining a tight blue light on Cassandra. The Faceless Rebels arrive and begin burning the people. Scully recalls "they have no faces, they have no eyes". Quiet Willy draws his gun and goes after the Faceless Rebels. Another triangular UFO, with a more complicated metal grid on the underside with more smaller white lights, coasts overhead the bridge. From its underside it fires several blue beams which hit the Faceless Rebels, igniting them on fire. The UFO then hovers over the people, shining lights on them. All the people including Scully reach into the air with their arms, but only Cassandra is levitated, she floats up from her wheelchair and up to the UFO.
Skinner meets Mulder and Scully about Scully's regression tape. Mulder says it was "described and then interpreted into a linear narrative, a gestalt impression of a subjective nonlinear experience", that it was a military staging and Cassandra was taken onto a military aircraft. Skinner says that aliens are a more plausible explanation.
Marita is still infected, Well-Manicured Man and the Syndicate Elders find. 1st Elder says "the Vaccine has no effect". Well-Manicured Man says "we must give it time". 1st Elder says "we must survive first. Survival means collaboration". Well-Manicured Man says "turn over the alien rebel, and you turn over any chance of resistance". 1st Elder says "it's already been done".
Spender learns Scully saw Dr. Werber, and shows her a tape of himself 11 years old, undergoing regression hypnosis: "there's a bright light, there's people standing around. They're looking up at something in the sky, where the bright light is... there's something in the sky, and it's got flashing lights, and its so bright it hurts my eyes. And then [Cassandra's] going up into the sky... and then I feel my feet, and they aren't on the ground. I'm floating up". Spender says his mother's stories created that 'memory' to replace the fact that his father left his family and it drove his mother insane, but he was 11 and didn't know it.
Mulder comes home to his apartment to find a note on the ground saying "things are looking up". Krychek charges him and slams him to the ground, putting a gun in his face. Krychek says "I'm not here to kill you, Mulder. I'm here to help you. You know, if it wasn't in my best interests, I would just as soon pull this trigger. Hear this, Agent Mulder, listen very carefully because what I'm telling you is deadly serious. There is a war raging, and unless you pull your head out of the sand, you and I and about 5 billion other people are going to go the way of the dinosaur. I'm talking planned invasion. The colonization of this planet by an extraterrestial race. Kazakhstan, Skyland mountain, the site in Pennsylvania. They're all alien Lighthouses where the Colonization will begin, but where now, a battle's being waged. A struggle for heaven and earth. Where there is one law: fight or die. And one rule: resist or serve". Mulder asks "serve who?". Krychek says "not who, what... I was sent by a man, a man who knows, as I do, that resistance is in our grasp, and in yours. The mass incinerations were strikes by an alien rebellion to upset plans for Occupation. Now, one of these rebels is being held captive. And if he dies, so does the resistance". Krychek shows his gun has no bullets, and hands it to him. Krychek kisses Mulder's cheek, and says in Russian "good luck to you, my friend". Krychek leaves.
Wiekamp AFB: The Pilot sneaks over the fence into the base.
Scully visits Mulder at his apartment; he has been sitting in the dark thinking about "destiny, fate... the inextricable relationships in our lives that are neither accidental nor somehow in our control, either". They are both reconsidering their new outlooks on life now. Mulder shows her Krychek's note: on the back it says "Wiekamp Air Force Base". Mulder says it is "maybe an answer, to a question you and I seem to have been destined to ask".
Wiekamp AFB: Mulder and Scully try to bluff their way onto the base, and Mulder is about to race through the gate when Scully recognizes the driver of a large military truck leaving the base as Quiet Willy. Mulder jumps onto the truck, and Scully gets arrested in the car. Mulder gets into the truck bed; it is empty except for a single coffin sized chamber holding the Faceless Rebel inside. After a distance from the base, Quiet Willy stops the truck and morphs back into The Pilot. He goes back into the truck bed, no Mulder. He draws out his Glimlet and is about to open the prison cell when a bright light appears overhead, and a Faceless Rebel holding a Lighter is teleported down to the truckbed with a white light. Mulder jumps out from hiding, screaming "no!" and shoots.
Well-Manicured Man checks Marita; the Black Cancer no longer runs through her eyes. He nods to the Syndicate Doctor.
Military Police storms the truck, finding Mulder sitting in the truck dazed. He gets arrested and thrown in a car with Scully. He says he doesn't remember what happened, and seems on the verge of tears.
Skinner tells Spender that Mulder has opened an X-File on Cassandra, but it won't reflect on his career, "it seems you have a patron outside this office who thinks highly of you... someone working with a high level of influence". Spender gets the letter from his father.
Canada: the letter is returned unopened by the boy to... Cancer Man.

Plot Points:

Cancer Man is alive and living in hiding in an isolated cabin in the Canadian mountains. He writes a letter to his son FBI Agent Jeffery Spender, but Spender returns it unopened. He is acting as a patron to help Spender's FBI career now.
Spender is the son of Cancer Man. His father left his family when he was 11.
Spender remembers under hypnosis regression being abducted alongside Cassandra as a child, but he thinks it false now.
At Ruskin Dam, the Faceless Rebels began burning abductees again, killing Quiet Willy and the Russian boy. A Colonist UFO appeared, which killed the Faceless Rebels with a flame beam weapon then abducted Cassandra before leaving. The survivors of the encounter were found in shock with minor burns and no memory of the encounter. The Faceless Rebel UFO later crashes at a West Virginia AFB where only one survives.
Colonist UFOs possess a blue flame weapon which can destroy Faceless Rebels.
Krychek allies with Well-Manicured Man and gives him the Russian Vaccine, which eventually cures Marita of the Black Cancer.
The Faceless Rebels are an alien resistance against the Colonists. They mutilate their faces to prevent Black Oil infection.
Well-Manicured Man is hopeful that resistance against the Colonists is possible with a successful Vaccine, and if not with that than by allying with the Faceless Rebels. The other Syndicate Elders don't believe this.
First Elder contacts the Colonists and tells them about the surviving Faceless Rebel; a Pilot is sent to execute the Rebel. Well-Manicured Man sends Krychek to Mulder, who gives him a speech about resistance being possible against Colonization, if he saves the Faceless Rebel.
Mulder finds himself in the middle of an encounter between a Pilot and a Faceless Rebel, both armed, over the surviving Faceless Rebel. He fires his gun, but has no memory of what happened afterwards.

Analysis:

Cancer Man thinks of a Navajo story, again connecting the Syndicate to the Navajo WWII code talkers ("Anasazi") who encoded the DoD alien files. Plus, it connects to his personal history with the seemingly Navajo First Elder.
Cancer Man is reminded of twin war gods coming to their father because of his relationship with his biological son Spender and his pseudo-son Mulder. Well-Manicured Man and First Elder seem to be familar with this story as well; Well-Manicured Man tells First Elder that now they have the weapons and the magic in hand.
Scully is found in vasogenic shock; this is when the blood veins constrict, which happens because of shock.
So after the Colonists saved the abductees, they fled into the forest as one group, where they were found huddling hours later by the search copters.
A Syndicate doctor says they've given Marita 3 intramuscular injections to no effect; she must refer to the American Vaccine which doesn't really work. She remains comatose. This is surprising, because in "Terma" we see people given the American Vaccine (and were infected presumably with Tunguska Black Cancer since they were so desperate to smuggle it out of Russia) and they are not comatose they are moving around talking but in a lot of pain. Maybe those test subjects were given miniscule amounts of Black Cancer (because they only had what little they could smuggle out of Russia) and Marita got a big gop of it, so the American Vaccine can 'deactivate' small amounts of Black Cancer but not large amounts; the Russian Vaccine can!
If, as Well-Manicured Man implies, the Russian Syndicate knows Krychek took this boat why don't they send an agent like Vassily Peskow ("Terma") to kill/retrieve him?
Well-Manicured Man says it was unwise to ally with Marita who was playing all sides, yet last episode he let her sit in and listen to the Elders talking about when Colonization happens!
So if Marita betrayed the Syndicate and Krychek, was she really on Mulder's side all along?
So Krychek infected Dmitri so if anyone betrayed him and tried to learn what Dmitri knew, they would get infected. This is a very poor assumption! It assumes that only one person would be there (only one person can get infected!) and really if someone like the Syndicate took him, would one of the Elders open the stitches themselves, or would they have a doctor do it who would then get infected not them?
Krychek makes a very strange turnaround in this episode. In his first scene, he doesn't want to give Well-Manicured Man the Vaccine and he thinks that the Vaccine won't stop Colonization. In his later scene, he has great respect for Well-Manicured Man and says how they must try to resist by saving the Faceless Rebel! Wait, maybe he thinks they should resist, but by allying with the Rebels and not with the Vaccine. Since he's from the Russian Syndicate, he would know a lot about the Russian Vaccine, and if he thinks it won't stop Colonization than Well-Manicured Man should be listening. After all, in The Movie Mulder injects the Vaccine into the Colonist Mothership, and while it forces it to leave the planet it doesn't mean that Colonization is over by far!
The Ruskin Dam incident takes place at night. A whole day goes by. Then the next night, the Faceless Rebel UFO crashes. Where was it for the 24 hours before that? And who shot it down? The Colonist UFO(s) which had arrived to handle the situation? The Syndicate/military defense grid (including the Warbird lazer satellites from "Kill Switch"?
Well-Manicured Man suddenly becomes an expert on the Faceless Rebels, while Second Elder doesn't know anything about them. Presumably this is because Krychek told him what he knew about the Rebels.
Well-Manicured Man calls the Faceless Rebels "resistance fighters", which suggests that they are a renegade part of the force they are fighting against, the Colonists. This is supported by the fact that they are visually identical to the Colonists' Pilots. In fact, perhaps the Pilots are a race that have been enslaved by the Colonists (by infecting them with Black Oil/Purity), and these Rebels are the few members of the species who haven't been possessed by the Colonists yet, and they are striking in revenge for the enslavement of their race.
Why is it that no-one except for Well-Manicured Man wants to ally with the Faceless Rebels? It seems that over the decades, they have consigned themselves to the destruction of humanity and think it's pointless to try resistance now. Cancer Man seems to feel the same way in "One Son". By Well-Manicured Man, like Bill Mulder, wants to work to prevent it. Notice in "Tunguska"/"Terma" he and Cancer Man are the only Elders who meet about the Vaccine Program, and in fact he says only six of "us" knew, so maybe he does this in secret from the majority of the Syndicate, because they have no interest in resistance. Then again, Cancer Man doesn't either yet he worked with the Vaccine Program there!
Just what does Quiet Willy except to be able to do with a gun and no gas mask against the Faceless Rebels?! He torched for his troubles, and rightly so!
The Rebel UFO and Colonist UFO look different, but have the same shape and general design, again suggesting that the Rebels are break-aways from the Colonists.
We next see Cassandra under Syndicate care, so the Colonists abducted Cassandra here then gave her directly to the Syndicate.
Maybe the Rebel UFO didn't stop and just dropped off 4 Rebels then left because it sensed the approaching Colonist UFO(s) so it had to run up into orbit to do battle with them!
Why DID the Colonists intervene here, when they didn't in the first two strikes? The Syndicate never called them about it on their Colonist Radio ("Talitha Cumi", "One Son"). Perhaps it was because at this strike was Cassandra, who is one of the Syndicate Elders' 'children' taken as part of the deal in "One Son" who is being worked on to become the Perfect Hybrid!
Obviously the Syndicate UFOs do not carry weapons, or else they would use them to fight the Faceless Rebels.
A Pilot/Faceless Rebel can also be killed by immolation, unless that Colonist blue flame weapon was something else.
So the Colonists can activate a signal which causes all abductees to be drawn to the nearest Lighthouse. Obviously the Faceless Rebels were able to fake this signal in order to draw together all the abductees in order to kill them, thus upsetting plans for Colonization.
If killing all the abductees will stop Colonization, why doesn't the Syndicate just let it happen?
Why does it take so long for the Vaccine to work on Marita, when it worked instantaneously on Scully in The Movie? Probably because Scully was infected with a miniscule amount from a bee while Marita got a big gop of it.
So First Elder went behind Well-Manicured Man's back and called the Colonists?! Isn't this a MAJOR breach of protocol? Should Well-Manicured Man retaltiate against this? Then again, maybe he ISN'T the superior to First Elder (he seems left out of the loop in the meeting with Syndicate leader Strughold in The Movie too). Then again, First Elder is just an intelligence man apparantly...
So Spender got abducted when he was 11? Does this mean he has an Implant? Very unlikely (he would have felt the calling to a Lighthouse last episode), he was probably just taken along with his mother.
Spender isn't very clear, but it sounds like his father left his family when he was 11. Obviously Spender wasn't born yet in 1973 because for Cancer Man Cassandra had to be abducted instead of a child because he was the only Syndicate Elder without a child. So let's be generous and say Spender was born in 1974. When he was eleven and Cancer Man divorced Cassandra, it would be in 1985. And that would mean that right now Spender is only 24 years old, can he really be in the FBI and have the same rank as Mulder (Special Agent)? Maybe it is thanks to Cancer Man's patronage, but what Skinner says at the end it sounds like Cancer Man just began helping Spender's FBI career in this episode.
So Well-Manicured Man learns the other Elders went behind his back and called the Colonists on the situation; they sent a Pilot to execute the Faceless Rebel. This means that the Syndicate doesn't have a Glimlit themselves, yet Cancer Man's assassins easily produce one in "Memento Mori" and "Two Fathers"! Maybe when Cancer Man 'died', he took with him all their Glimlets!
Anyway Well-Manicured Man sends Krychek to get Mulder to save the Rebel from The Pilot, so that he can ally with it. He does this because if Mulder does it, the Syndicate won't get in trouble with the Colonists because they know how Mulder is operating by himself. In fact, this is a brilliant manuever! Anytime the Syndicate needs to do something that would piss off the Colonists, trick Mulder into doing it!
Obviously the Syndicate doesn't have a Glimlet because Krychek would have given Mulder one.
Once Mulder sees that The Pilot is about to execute the Rebel, what does he expect to do? He has miraculously lost his Glimlet from "Herrenvolk" (which would be a shame because it would be VERY handy here!) so did he just plan on shooting from a distance or something? Here's a theory: if you shoot your gun into the base of The Pilot's neck, would it hurt him?
The Faceless Rebels have teleportation abilities. In fact, that explains why the Rebel UFO just coasts over and past the Ruskin Dam bridge, they teleported down the 4 Rebels while everyone was staring at the UFO.
So who did Mulder shoot? Presumably The Pilot since he was sent to save Rebels, but from his angle it looked like he was aiming at the Rebel rescuer!
So what happened? Here's the most likely scenario: Mulder shoots The Pilot. The Pilot ignores Mulder. The Rebel ignores Mulder. The Rebel rushes The Pilot with his Lighter. The Pilot tries to grab his Lighter from him. There is a struggle, but eventually the Rebel is able to torch The Pilot, which kills The Pilot. The Rebel then frees the captive Rebel. Meanwhile Mulder is just watching on in shock.
Then again, why would the Rebels bother to wipe Mulder's memories of the encounter. It was the Colonists who wiped the memories of the abductees at Ruskin Dam (since they were the victors and still there afterwards), and when it was only the Rebels at the Russian strike Dmitri retains his memories of the encounter.
In fact, Mulder's missing memory suggests that the Colonists somehow won that encounter! This is supported by "Two Fathers"/"One Son", because in those episodes the Faceless Rebels return to Earth and destroy the Syndicate, so obviously they didn't make friends which Well-Manicured Man was supposed to do with them if the Rebel captor survived.

TRAVELERS

The Run Down:

1952: FBI Agent Arthur Dales and his partner Michel arrest Edward Skur at his home for failure to appear before HUAC, Michel plants a Communist party card. Later Michel tells Dales that Skur hung himself in his cell. Dales goes to the Skur home to tell his wife, but instead he sees Skur and chases him. Skur pins him, and some crustacean creature begins to come out of his mouth before he runs away. Michel tries to convince Dales that he was drunk, but Dales already filed his report. Dales is called in to see Roy Cohen, Special Assistant to the Attourney General in the Justice Department, a HUAC heavy. Cohen says in war secrets must be kept, and orders him to take Skur's name out of his report. Dales agrees, but Skur had already murdered someone by then.
Michel brings Dales in on a homicide call from the local police, but when they arrive at the house there are no police. The victim was a German doctor, high-ranking enough to be shaking hands with the President in a picture. Police arrive; they say they didn't call them over and just learned when his nurse called saying he didn't show up for work. Dales sees a note for a meet; it was left by Bill Mulder, who had already been at the crime scene. Dales meets Bill Mulder; Bill warns him about Skur. He tried to save the doctor but he was too late. Bill says Skur isn't a communist, "he's a patriot. All of these men are patriots". There were 3 men- Skur, Gissing, and Oberman. Those 2 are dead, they killed themselves because they couldn't live with "what they'd been turned into", Skur is the last one and his escape threatens everything. Bill says "I risked my career and my family by coming here. But the crimes these men have committed against innocent people, I can't have that on my conscious anymore. Someone needs to know the truth". Skur is after vengence against the men who did this to him but "he can only guess at the dimensions of this conspiracy", and he thinks that Dales and Michel are part of the conspiracy.
Skur kills Michel at his home; the crustacean creature crawls from Skur's mouth into Michel's. Michel's body looks like it was force-fed acid. Cohen arrives and takes the body, threatening labelling Dales a communist if he interferes. Dales investigates the 2 other men but the HUAC report is all censored up. Dales learns about the X-Files from a secretary who, under Director Hoover's orders, files certain reports to be forgotten under "U", then under "X". Another German doctor, Strohman, died mysteriously. One of his patients, Gissing, found dead of suicide at the scene. Gissing's body is still in the morgue only because he was a StateDept bigwig and his family is making a stink about taking the body. Dales examines the body; there are recent surgery marks and a sluggish but still moving crustacean creature is sutured into his throat.
Skur was a patient of the same doctor; Dales visits Skur's wife and says Skur is alive and his surgery for 'war injuries' was anything but. "It's called xenotransplanation. It's the grafting of another species into the human body. It's a procedure that Nazi doctors experimented with during the war, and I believe they continued their work here". Cohen arrives and takes Dales with him. Skur's wife visits Skur, who is hiding in the basement. Skur says it's too late to help him, and attacks her.
Cohen takes Dales to see Director Hoover. Hoover gives a speech: in 1945 the American-Russian ratio was 9-1, but now it is 5-8. "The threat of global communist domination is a reality that can be ignored only at the risk of our own annihilation. If we are to defeat the enemy, we must use their tools. We must go farther. We must do those things which even our enemies would be ashamed to do. It is only through strength that we can make our enemies fear us, and thereby ensure our own survival". Hoover gives Dales one last chance to prove himself a patriot and save himself...
Dales is in a car getting instructions from Bill Mulder to meet with Skur and put him at ease, they'll come in when the time is right. Bill Mulder says "I follow my orders". Dales goes into the bar unarmed to meet Skur. Skur says they're not coming, they want him to kill Dales. Skur attacks Dales. Bill Mulder wants to intervene but his associates hold him back. Dales manages to handcuff Skur to the bar. Dales' career was ruined after that.
Later, Bill Mulder drives Skur out alone to the countryside. He frees Skur and gives him the car. Skur escapes.
1990: During an eviction Skur is shot and killed. His dying word is "Mulder". A body is found in his house with all the soft tissue removed. Mulder visits the retired Dales about his Skur X-File. Most of Dales' report has been censured but Mulder knows Skur disappeared 38 years ago during a case about victims with their internal organs removed. Dales points him to HUAC (House Un-American Activities Committee) who hunted communists in the '40s and '50s. Dales says they found practically nothing but "do you think they would have found nothing unless nothing was what they wanted to find?".
Mulder reviews a HUAC tape and sees his father in the group. He returns to Dales wanting the truth, he doesn't "really speak" with his father. At further urging Dales said that Skur, like Bill Mulder, worked at the State Department. He was a labelled a communist so the FBI (ie Dales) went after him. Dales tells the story he knows. Mulder says "I can't believe that my father threw in with these men. He let them dictate his conscience". Dales says someone probably released Dales, "in the hope that by letting him live, the truth of the crimes that were committed against him and the others might someday be exposed".

Plot Points:

In 1952, Bill Mulder and his associates were involved with an experiment. German 'Paper Clip' doctors grafted an alien-like crustacean creature into the throats of 3 State Department men. It gives them murderous urges, and the creature leaves their throat and jumps into the throat of the victim, where it consumes all the internal organs with an acid-like substance.
In 1952 Bill Mulder was disgruntled with his work, so he informed to Dales and set free a test subject so the truth might be exposed.
Enter Arthur Dales: an FBI Agent who in 1952 investigated Bill Mulder's experiment, which ruined his career.
In 1990, Mulder met Dales and learned how his father was involved in this experiment.

Analysis:

Obviously Michel was a Pre-Syndicate plant the whole time, working to coverup the Skur affair. Dales never realized though, but Michel was the one leading Dales around by the nose the whole time.
Of course these German scientists were from "Paper Clip" like Victor Klemper, brought over to work for the Pre-Syndicate to make an alien-human Hybrid.
So that note at the dead German doctor's place from Bill Mulder probably was for the doctor but he was dead and Dales just happened to see it.
Gee, isn't it amazing that the Pre-Syndicate wasn't able to steal Gissing's body just because his family was making a stink about it? This is the secret government in the Red Scare for god's sake!
Even more ridiculous is that they didn't remove the crustacean! Surely they could take that and leave the body!
So were people like Hoover, Cohen, and McCarthy actually part of the anti-alien conspiracy Pre-Syndicate? It seems more like they were being used by the Pre-Syndicate, who claimed they were a conspiracy working against the communists. When Hoover talks about going farther than their enemies would he's obviously talking about Russia and not the aliens. So for this experiment, the Pre-Syndicate probably told these people they were trying to make a killing machine for war or something.
This experiment seems like the very first alien-human Hybrid experiment. It's only 7 years after WWII, only 5 years after Roswell (it still appears this was where the Pre-Syndicate first learned about the aliens). Of course in the '50s genetic engineering was hardly invented, DNA just recently discovered, so all they could manage to do towards their goal was to sew that thingee into their throat!
So what WAS that thing? Was it an alien creature salvaged from a UFO wreakage? Is this alien one of the Colonists, holding Black Oil? It had to have been alien because it could secrete that acid-like liquid and digest internal organs!
How did Bill Mulder cover-up the fact that he checked out Skur from wherever they were holding him, drove him out and let him escape? Or maybe he said Skur managed to over-power him and steal the car.
So the whole Red Scare with HUAC was the Pre-Syndicate creating a big distraction to coverup their experiments. In fact, since nowadays their cover is ridiculous alien abductions, maybe this was the same concept!
So in 1990 Mulder learned that his father took place in covering up what was likely a government experiment with aliens, yet in "Ansazi" Mulder seemed to have no clue about this. Then again at the time he was hopped up on LSD...

THE PINE-BLUFF VARIANT

The Run Down:

Mulder is secretly recruited by a FBI-CIA taskforce to infiltrate a right wing militia group which has a highly acidic biotoxin delivered by aerosol. Mulder is 'recruited' by the 2nd in command Haley and a suspicious Scully investigates, but gets warned off by Skinner and a CIA agent. They inform her Mulder's in a deep-cover assignment previously known only to Skinner and the Attourney General. Mulder got recruited by the milita after one of them heard his government conspiracy rant at the Boston UFO Conference in "Patient X".
The militia leader Bremer tests the biotoxin at a movie theater. Bremer is also personally keeping electronic surveillance on Mulder's apartment, where he hears Mulder and Scully talking about his undercover assignment.
Mulder gets his left pinky broken in an interrogation secession with Haley to see if he's for real. Once he's proved his worth, Haley asks him for information on bank money movements. The CIA agent has ready-made false papers for it. Scully learns the biotoxin is a genetically-engineered virulent strain of streptococcus, too advanced for Russian biowarfare. CIA says its Russian. The US officially stopped biowarfare programs in 1969, but Scully tells Skinner the biotoxin is an advanced descendent of a bioweapon made by the Army's Pine Bluff Facility in the '60s.
Mulder and the militia robs a bank. Bremer sprays the remaining money with the biotoxin and saves Mulder from having to kill a hostage by saying Mulder's gun is traceable and killing the hostage himself. After the heist Bremer burns the stolen money. Bremer puts a gun on Mulder, but Haley says Mulder gave him the docs proving Bremer's been leaking to the FBI for 2 years about them. Bremer plays his surveillance tape of Mulder and Scully discussing his undercover assignment. Bremer holds Mulder and Haley prisoner. He gives Haley a pair of keys for a car and lets him escape. He takes Mulder out with one milita man to execute him, but instead kills the milita man and gives Mulder a car to escape. Later Haley dies of the biotoxin in the car, which was on the keys.
Scully realizes the milita is infecting the money and finds the bank they robbed by recognizing Mulder's broken finger. The money is quartined before it's touched. The CIA agent says the money is clean and will be used as evidense against the milita. Mulder accuses the CIA agent of killing innocent citizens, he says "sometimes our job is to protect these people from knowing" the truth.

Plot Points:

A CIA man infiltrated a right wing milita group, became its leader, then used it to test an genetically engineered Army bioweapon, a virulent strain of streptococcus which the Army is not allowed to make. Mulder was used to infiltrate the group.

The Run Down:

There doesn't look to be any Syndicate involvement here, just the usual military-industrial complex which works with the Syndicate but has no idea about their true motives and goals.
So the US goverment continues to make bioweapons illegally and secretly. There's a shocker!
It seems likely that it was Bremer who pushed to have Mulder recruited into the milita since the whole thing was a CIA plot.
So at first, only the Attourney General and Skinner knew about Mulder's undercover operation. This is interesting, because in "The End" (two episodes from now!) the Attourney General has the X-Files closed and Mulder and Scully reassigned! In fact, the Attourney General seems in with the Syndicate and/or military-industrial complex.
They never say it outright, but assumedly Bremer sprayed the money at the movie theater, and then when people bought food and drink they got the contanimated food. The two boys who snuck in didn't buy any food so they didn't get infected. Gee, isn't it amazing that EVERYONE else bought food or drink?
The first time we see the biotoxin, it almost immeadiately kills its victim. The movie theater must have taken five to ten minutes (enough time for them to get to their seats), and Haley drives for some distance before dying. So presumably Haley just put a lot of biotoxin on the first guy and the rest got miniscule amounts.
So was the bank money infected or not? If it wasn't as the CIA agent claimed, what was the point of the heist? Perhaps the whole thing was not to test the biotoxin (perhaps that was the movie theater but then again Bremer didn't need to be with the milita to that test but he must have joined the milita so they would have gotten the blame for the biotoxin) but to get rid of Haley so Bremer would have absolute control of the militia.

THE END

The Run Down:

A young boy, Gibson Praise, plays chess with a Russian man in a stadium. A Gunman sets up an sniper rifle in the rafters, and Gibson seems to sense him. Gunman shoots but Gibson moves, and the shot hits and kills the Russian.
Canadian mountains: two men parachute drop to Cancer Man's cabin. Cancer Man's alarm goes off and he shoots one man with a shotgun then flees into the mountains. The second man, Krychek, catches Cancer Man after a shot at him. Cancer Man is flustered and tells him to shoot. Krychek says "I was sent to bring you back".
Gunman is quickly caught; he's former NSA and his gun was registered to a US intelligence agency. Agt Spender is given the case "as an order from somewhere outside the Bureau" and requests Mulder is excluded, so Skinner brings him in on it. Scully and Special Agent Diana Fowley are there. Mulder points out how Gibson moved so the bullet didn't hit the back of his neck, instead hitting the Russian. Fowley backs his theory up.
Krychek takes Cancer Man to see Well-Manicured Man and the Syndicate Elders. The Elders said they thought he was dead, too much blood was lost. Cancer Man says "obviously you underestimate me, more obviously you overestimated the man you sent to do the job. Well, let's say all if forgiven. Now, you have a job for me". The matter is the boy who "is a problem to us". Cancer Man asks if he is to kill the boy, which offends Well-Manicured Man. First Elder says "it's in your interests, as in ours". Cancer Man says "you think you know my interests?" but agrees to take the job.
Fowley has been in Europe working on foreign terrorism since 1991 when the Berlin Wall fell, and when Mulder began working on the X-Files. Mulder, Scully, and Fowley meet Gibson. Gibson refuses to play an electronic chess game; Mulder asserts he reads the minds of others that's how he wins at chess and how he knew about Gunman. Gibson reads Mulder's mind and says he has a dirty mind, that he and one of the 'girls' he brought are thinking about each other. Mulder orders protection for the boy. Scully says never in the X-Files have they met a true telepath, they were all fakers. Fowley says whoever wants to kill is in the business of keeping secrets.
Mulder talks with Gunman; his career includes Special Forces training, operations in Grenada and Zaire. He was inside Hussein's palace in Iraq when the bombings began but he failed to kill Hussein. Mulder says he was sent to kill the boy because he can read minds, and offers witness protection or immunity in return for his testimony. Gunman says it'll never happen. Later the Gunman receives a Morleys cigarette wrapper which says "you're a dead man".
Scully and Fowley test Gibson; he reads the minds of the doctors. Fowley says she witnessed telepathy demonstrated and 90% accurate clairvoyants when she and Mulder were working psychiatric hospitals, meeting patitents with criminal setences who they thought were misdiagnosed. Fowley later tells Mulder the tests show Gibson can read several minds at once.
Scully visits the Lone Gunmen to examine Gibson's brainscans. She asks about Fowley; she was Mulder's girlfriend out of the Acadamy and discovered the X-Files with him, with a para-science background.
Cancer Man meets Spender, and says he's taken an interest in him and gave him this case. Spender asserts he's CIA or NSA and asks what information he said he has. Cancer Man says "control the board. Know which men to sacrifice and when. Don't become a part of someone else's cause or crusade. Pursue your own self interest. Always". Mulder briefly sees Cancer Man who flees, and accuses Spender of lying to him. Mulder tells Spender he thought he was dead.
Scully presents to Skinner, Mulder, Spender, and Fowley. Gibson has unheard of brain activity in his 'God module', an area of the temporal lobe that neurophysicists are only beginning to understand. Mulder says all famous thinkers may have had unheard of brain acitivity like Newton, Galileo, Einstein, Hawking. "This kid may be the key not just to all human potential, but to all spiritual unexplained paranormal phenomena. The key to everything in the X-Files". Mulder wants to get Gunman immunity for his testimony, which Spender is disgusted with. Scully says it's quantifiable proof of the X-Files. Fowley warns that if they do this, the Attourney General will get pissed. The X-Files are open as an indulgence, attracting the wrong attention will close them. Mulder has Skinner call the AG.
Mulder meets Gunman; the AG needs more information for immunity. Gunman says "the kid is a missing link", Mulder asserts he's genetic proof about unexplained dormant inactive genes are from "alien astronauts" and that he is part alien.
Well-Manicured Man meets Cancer Man, driven by Krychek. Well-Manicured Man says he's failed, Mulder's gone to the Justice Department with testimony about the boy. Cancer Man says "that's just part of the game... It's all a game. You just take their pieces, one by one until the board is clear". Well-Manicured Man is disgusted. The Gunmen gets another Morleys wrapper; it's blank. The prison guard shoots Gunman.
Fowley is protecting Gibson in a hotel room. Gibson says there's a man with a gun who's aiming at her. She stands and gets shot in the chest. A US Marshall was also killed outside. Gibson is gone. The Gunman's body was also found with the blank Morleys wrapper.
Cancer Man produces Gibson to Well-Manicured Man and Krychek. Gibson calls Cancer Man and Well-Manicured Man both liers, which surprizes them. Cancer Man says "you've never had the stomach for our business. I'm a neccessity. The complement to your cowardice. My work is just beginning". Well-Manicured Man gets in the car with Gibson, driven by Krychek. Krychek offers to kill Cancer Man, but Well-Manicured Man says "no, he's useful. And you may need him in the future".
Mulder attacks Spender, pushing the Morleys wrapper in his face saying he's working with "Old Smokey" and he's gonna make sure he's prosecuted for murder, his days are numbered. Spender says that Mulder's days are numbered to himself.
Mulder and Scully are in serious trouble with the AG, Skinner is trying to defend them because of their personal involvement but the AG isn't interested. Spender is also screwing Mulder, quoting his "alien astronauts" assertion. There are talks about reassigning Mulder and Scully, and closing the X-Files at the Justice Department's behest. Fowley is in critical health. Mulder says "this was all strategized, every move. I just couldn't see it. It was all of a plan".
Cancer Man visits Mulder's office and takes the X-File on Samantha. Cancer Man runs into Spender, who asks who he is and how he got in here. Cancer Man says "it's all about access. It's what I can give you. It's what can make you. It's why I'm doing this for you. I'm your father". Spender is shocked, but fire alarms ring out and Cancer Man leaves. Mulder's office gets torched in a fire, and everything, including the X-Files, is destroyed.

Plot Points:

Enter Gibson Praise: a young chess prodigy boy with telepathic powers. He can read several minds at once. His 'God module' is active; he has unheard of brain activity. The Syndicate tries to kill him but fails, but Cancer Man is able to abduct him and gives him to Well-Manicured Man.
Gibson is the first known true telepath, and is a genetic link between humans and aliens. Mulder thinks he is the answer to unexplainable dormant genes in all humans, as in alien ancestors. He is the key to all human potential and all unexplained phenomena; he is the key to the X-Files.
Enter Agt Diana Fowley: Mulder's old girlfriend out of the Acadamy who discovered the X-Files with him in 1991, before that they investigated clairvoyants and telepaths in mental institutions. She's just returned from Europe where she worked on international terrorism since 1991. She is shot and critically wounded protecting Gibson.
Krychek is now acting as Well-Manicured Man's right hand man and recruits Cancer Man back to the Syndicate for him.
Mulder briefly sees Cancer Man alive and with Spender; he now knows Spender is a pawn of Cancer Man.
Gibson's would-be assassin offers testimony about Gibson in return for immunity. Mulder asks for his immunity from the Attourney General. When Gibson disapeers, the assassin is killed, and Fowley is critically injured, Mulder is in serious trouble with the AG. There are talks of reassigning Mulder and Scully and closing the X-Files.
Cancer Man tells Spender he is his father and offers him power.
Cancer Man torches Mulder's office and the X-Files, taking with him Samantha's X-File.

Analysis:

It's amazing the feats that the one-armed Krychek preforms in this episode! He does a parachute drop, drives a car expertly, wow!
So here the Syndicate uses a former NSA assassin (this is when Cancer Man is no longer part of the group). In "731" someone sends a NSA assassin to stop Ishamaru's work, in the same episode First Elder plays a prominent and independent role, and the BlackOps troops are seen in that same two-parter. In "Paper Clip" when Cancer Man fails to do his work, First Elder calls in "our friends" who are either armed troops driving CIA cars or aliens. So maybe this means that First Elder is connected with the NSA (which is also BlackOps) and that with Cancer Man gone First Elder is handling the assassin work with his old NSA buddies.
So Cancer Man hints that his interests are not the same as the Syndicate's. What does this mean? Perhaps it means that while the rest of the Syndicate wants to resist Colonization, Cancer Man is happy to have it go ahead. We see Cancer Man's willingness to let it happen in "One Son", but then again in "The Red and the Black" we see the other Syndicate Elders preferring to collaborate with the Colonists rather than take a chance on resistance. Or perhaps this simply refers to his obsesssion with his son and pseudo-son.
Mulder graduated from the FBI Acadamy in 1988, and was assigned to the Violent Crimes Unit. In 1991 he began work on the X-Files, in 1992 Scully was assigned to debunk his work. So in the Acadamy Fowley was his girlfriend, and in 1991 she worked with him on the opening of the X-Files, but left for Europe in that same year.
So it seems that near the begining of 1991 Mulder and Fowley opened the X-Files and worked on them, appearing to first investigate clairvoyants and telepaths in nut houses. Then near the end of 1991 Fowley left him (was this when their relationship ended?) and went to Europe, from where she just returned.
In "Unusual Suspects" we saw Mulder was a normal guy until 1989 when he in a hallucination he saw aliens and learned conspiracy theories from the Lone Gunmen. In that same year he underwent the hypnotic regression with Dr. Werber and remembered Samantha's abduction. In 1990, Mulder investigates his father's suspicious past.
In 1989 "Unusual Suspects" Mulder has a wedding ring on, but his FBI file says he's single. This must mean he was engaged to Fowley and just wanted to wear the wedding ring for some reason but they broke up and she went to Europe near the end of 1991.
So an NSA assassin team was in Hussein's palace when bombs began falling on Iraq but Hussein survived; this is another hint that Hussein is a US plant as Morris Fletcher revealed in "Dreamland II" and which was hinted to in "Terma" and "Three of a Kind".
Obviously Cancer Man has begun to take a fatherly role to Spender now that he's back from the dead and has rejected his pseudo-son Mulder. He spouts conspiratorial advice to Spender, gives him this assignment, offers him a deal for power.
This whole episode is also a masterminded Cancer Man plot to screw over Mulder; through Cancer Man's machinations the X-Files are closed, Mulder and Scully are reassigned, and he personally torches Mulder's office! Obviously he no longers cares for Mulder the way he once did in "Redux II"!
Cancer Man tells Spender to never become a part of someone else's crusade: Spender does this in "Two Fathers"/"One Son" by joining Mulder's crusade and Cancer Man kills him for it. He should have listened!
How in the hell can Gibson's active God Module and telepathic abilites explain EVERYTHING in the X-Files?! How does it explain ghosts and possessions? Werewolves? Vampires? TIME TRAVEL? What an exaggeration!
What the hell was Mulder thinking...? The testimony of a murder is going to prove Gibson is a telepath?! First of all, why would they trust anything he says, second of all what do you need his testimony for you have physical proof in Gibson!
How does this lowly assassin know the truth about Gibson? Why would the Syndicate bother to tell him this? Why not just order him to kill the boy and not explain why? Boy, they do need Cancer Man back, but then again he was just as bumbling as they are!
We learn more about these dormant inactive genes in humans that maybe part alien in "The Beginning".
Why oh why does Fowley stand when Gibson tells her there's a gun on her? It's the most idiotic thing and it gets her shot! There's only one possible explanation. We learn from "Two Fathers"/"One Son" that she's is in with Cancer Man. So maybe she let herself get shot so the Syndicate could steal Gibson without her getting in trouble. It's unlikely getting shot in the lung and being on the verge of death was part of the plan though!
As a matter of fact, since Fowley has been in with the Syndicate all this time, perhaps her return in this episode was part of Cancer Man's scheme to screw over Mulder. But she seems to truely care for him, why would she go along with this?
Why are Cancer Man and Well-Manicured Man surprized when Gibson says they are both liers?! They obviously don't trust each other at all or what they say! Hell, in "Apocrypha" Well-Manicured Man learned that Cancer Man lied to him about the DAT tape!
Well-Manicured Man tells Krychek that he may need Cancer Man in the future. This statement is very strange. First of all, it makes it sound like they are equals but Krychek is obviously his subordinate. Second, it shows that Well-Manicured Man is aware of Krychek's scheming double dealing and is encouraging it. Unfortunately we never get to hear more of this because Well-Manicured Man gets killed in his next appearance, The Movie.
The Attourney General isn't neccessarily in with the Syndicate. Mulder, who doesn't exactly have a good reputation, wants to free a murderer on ridiculous testimony. Then the murdered gets killed, the kid is kidnapped and his protecting agents get killed and critically wounded! Makes perfect sense she'd want to get rid of the X-Files if this is the kind of thing that will come from them!
Even though Cancer Man has rejected Mulder, he still cares for Samantha enough to take her X-File. Or maybe he just covering up evidense. This might suggest that Cancer Man is Samantha's biological daughter, but it's more sentimentality.
Cancer Man seems to offer Spender a deal for power here, which, we see in "The Beginning", he has taken him up on.
Surely the entire totality of the X-Files files are not sitting in file cabinets in Mulder's office! It's ridiculous to think there wouldn't be copies elsewhere and computer files as well. But unfortunately we learn in "The Beginning" that there really WAS only the single copies in Mulder's file cabinets! Ridiculous.

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