X-Files Mythology Guide Season Two

Mythology Guide: Season Two

LITTLE GREEN MEN

The Run Down:

Mulder narrates... in 1977 the two Voyager probes were launched, bearing a primer on humanity and Earth greeting whoever hears this in peace and asking them to visit us. 13 years later the probes left the solar system. In 1992 NASA began the high-resolution microwave survey; a decade long search for alien signals at places like the Arecibo observatory. One year later a Senator passed a bill which terminated the project, closing the Arecibo observatory. Humanity wants to believe but their eyes have been closed and they are now deaf the realms of extreme possibility. Mulder wants to believe but the tools have been taken away with the closing of the X-Files.
In the Arecibo observatory, long dormant computers come alive to monitor a broadcast: it's the Voyager signal.
Mulder is working on transcribing wiretaps and Scully is teaching autopsies at Quantico FBI training center. Mulder's spirit is broken.
Scully contacts Mulder and they covertly meet. Mulder watched Deep Throat's funeral at Arlington from binoculars. He knows they are being watched. Mulder is doubting his beliefs now, because of his time with Scully he now needs evidense to believe. He mentions astronomer George Halle who built the world's largest telescope in 1948 after an elf climbed in his window and told him to. Mulder is even beginning to doubt his sister Samantha's abduction by aliens...
Mulder's flashback to Samantha's abduction: Nov 27, 1973: young Fox and Samantha are arguing while watching the Watergate hearings, their parents are away for the night visiting friends. The house begins to shake. Red and blue lights appear outside the window. A bright light appears at the door which opens by itself. At the door, barely visable through the glare, is a Willowy Grey. Samantha is levitated and unconsious/paralyzed/shocked and begins to float towards the door. Fox grabs the family gun but is paralyzed and cannot fire. Samantha floats out the door.
Mulder is brought to see Senator Richard Matheson, who comments on a Bach concerto which was the first choice to go on the Voyager probe, saying he wishes it was the first thing aliens learned about humanity. Mulder says he's let Matheson down, who supported him "at great risk to your reputation". He knows when the X-Files were shut down there was nothing he could do. Matheson hands him a note: they may be listening. Matheson tells him to go to Arecibo, he will hold 'them' off as long as possible but he probably only has 24 hours. The Blue Beret UFO Retreival Team has been authorized to display terminal force. Mulder asks what he is looking for: Matheson says "contact". Matheson gives him an electronic readout of the signal.
Skinner asked Scully about Mulder's whereabouts but she didn't know and was concerned. He later plays the tape of this conversation to Cancer Man, who is confident that Scully will find Mulder.
Mulder arrives at Arecibo, where the control room is locked up. Inside the power is cut but systems are on, the air is stale. Inside the bathroom he finds a terrifyed Spanish man who says he saw red, blue, and orange lights in the forest. He went there and saw "men... like animals... but not men. They took me and put me here. They're still out in the woods!". Mulder finds the original signal came from beyond lunar distance, but the next signal came only miles away. The Voyager signal is broadcast again ("I send greetings on behalf of the people of our planet...") and the Spanish man freaks and runs out into the forest. Mulder later finds him dead, from fear.
Scully searches Mulder's apartment and finds the electronic readout, but has to elude two men keeping Mulder's apartment under surveillance. Scully learns the signal is like the WOW signal of 1977, an unidentifyable electronic signal that is the closest evidense of alien civilization. The WOW signal was 30 times greater than the background noise, came like morse code, and turned itself on when in the beam of the dish. She gets a list of SETI observatories and a list of flight charters, finding Mulder under the alias George Hale. Scully looses a pair of tails at the airport and heads for Puerto Rico.
Mulder examines the Spanish man and records it on a tape. No punctures (like in alien abductions), no lightening strike, but rigor mortis happened in only half an hour... he was frightened to death. Mulder says to the tape (for Scully) that he used to only trust himself, now he only trusts Scully, and he wonders what he would do if he actually met them, when he has been searching for them all his life. A rumble and screaming noise begins, with red and blue lights outside. A bright light shines through the window, another (non-audio) signal is being sent, then Mulder's recording is played back to him ("Trust No One") over and over. The door flings open and wind flies in. Mulder slams the door shut and the disturbance goes away for a while then returns. The door's lock open by itself and the door opens. Mulder grabs his gun as the Willowy Grey appears at the door. He pulls the trigger, but the gun will not fire.
Scully find Mulder the next day just before the Blue Beret team arrives. The Blue Beret team opens fire on Mulder and Scully, but after a lengthy cross-country car chase they are able to escape the Blue Beret team.
Skinner is chewing out Mulder for abandoning his post, threatening him with censure, transfer, suspension, probation while Cancer Man watches silently in the background. Mulder accepts punishment but says that he had enough to prosecute months ago but was being kept down and that his phone was illegally tapped. Skinner is shocked to hear this and looks at Cancer Man. Cancer Man says to Mulder "You're time is over. And you leave with nothing!". Skinner angrily orders Cancer Man out then tells Mulder to return to his assignment without punishment but orders him to continue the surveillance without prosecuting.
Mulder's tapes and recordings of evidense were all wiped by the close encounter.

Plot Points:

An group of aliens (Willowy Greys) identical to those who abducted Samantha are broadcasting the Voyager signal to Earth, first from beyond the Moon and then miles away from the SETI site at Arecibo. They wait in the wood and encounter a frightened native then place him in the locked control room at Arecibo.
Mulder is running wiretap surveillance and Scully is teaching at Quantico. They are not allowed to see each other.
Mulder watched Deep Throat's Arlington funeral through binoculars.
Mulder now requires evidense to believe because of his time with Scully, he even doubts his sister's abduction.
November 27, 1973: Samantha is abducted by a Willowy Grey in front of young Fox's eyes. The alien exhbits telekinesis and some form of telepathy that paralyzes Fox and Samantha. Guns will not fire in the aliens' presence for some reason.
Mulder's friend in the Senate, Senator Richard Matheson, may be under surveillance.
Matheson sends Mulder to Arecibo to make contact with the aliens. The Blue Beret UFO Retrieval Team will be there in 24 hours after he delays them, and they will kill Mulder.
Cancer Man is very concerned about Mulder's disappearance and searches for him through Skinner.
The aliens visit Arecibo and the native who previously met them dies of fear.
The aliens then visit Mulder, who tries to shoot the visitor but his gun does not work.
Mulder with Scully's help escapes the Blue Beret team.
Mulder could be transfered/fired but when Skinner learns Mulder's phone was illegally tapped he orders out Cancer Man and does not punish Mulder.
Mulder's evidense of the vistiation was wiped during the alien encounter.

Analysis:

A Senator leads a bill which kills the SETI project in '93. Sounds like the Syndicate was behind this (they have excellent Senate connections) and they would obviously want the rest of the world not to notice the occaisonal UFOs and communiques between the Syndicate and the Colonists that are flitting about all the time.
If the Syndicate is so afraid of the rest of the world getting a real look at the cosmos, why did they allow the Voyager probes? Perhaps they have first peek at the Voyager broadcasts so they could quietly delete any UFO apperances.
If there really was no power going to Arecibo, was the alien signal somehow transmitting power to the machine, enough to activate it?
PLOT HOLE: If Mulder watched Deep Throat's funeral, then he would have to KNOW HIS NAME!
1948: the world's largest telescope is built after a man sees an elf climb in through his window and tell him to. That's one year after Roswell, and what will become the Syndicate (call it The Group) has not allied with the Colonists and is just learning the secrets of the aliens from their UFO wreakage. Seems like they would be VERY interested in having a better view of the cosmos. Then again a small elf sounds like a Lil' Grey (as the Colonists appeared at the Syndicate-Colonist alliance meet in "One Son") which wouldn't fly, unless the hypnotized the poor shmuck. Their crude attempts at alien-human Hybrids looked nothing like the real thing.
Since Colonists abducted Samantha ("One Son") and Colonists met the Syndicate ("One Son"), we conclusively know that Purity likes to take different forms. The Samantha abductors are Willowy Greys and the Syndicate meeters are Lil' Greys.
The Syndicate is keeping surveillance on Senator Matheson, and apparantly he gives Mulder this information against their wishes. But like Deep Throat, Matheson was most likely doing the Syndicate's work here, or more specifically Cancer Man's work. Mulder was questioning his faith in this episode, which is bad for Cancer Man because he wants Mulder to be a crusader undermining the credibility of the believers, so he has Matheson, who he holds power over (and Matheson isn't happy about that!), engineer an alien encounter for Mulder. This also means that Mulder isn't being protected by the Senate... he's being protected by Cancer Man!
If this is true, Cancer Man is running a risky business. The Grey that lands cannot be a Colonist since the BlackOps troops come to kill it and the Syndicate would never let them kill a Colonist EVER. Because of the Security Counsel Resolution ("E.B.E." and "Musings of Cancer Man") and the Colonists not wanting the Syndicate to socialize with other aliens who might convince them to fight the Colonists, this alien must be killed when all he wants is to meet humanity and say hello. So Cancer Man must whisk Mulder in there and then whisk him out so the alien can be killed.
As such Matheson saying the troops are to use terminal intensity could be a lie of Cancer Man to scare Mulder away after the encounter, so the alien can be executed without Mulder present. If Matheson was telling the truth, it more likely meant the troops were ordered to kill the alien and he didn't kill Mulder. On the other hand, the BlackOps troops in "Paper Clip" had no problem trying to kill Mulder so they shouldn't have that problem here. The main problem stems because Cris Carter didn't come up with the Cancer Man- Mulder family connection until the end of the Second Season so Cancer Man's overtly aggressive actions here are a bit out of place.
At first the appearance of Jose Conception in a bathroom in a locked room is very suspicious, but a translation of what he says revealed he saw the aliens land and went into the trees to investigate, where he saw them and they apparantly transported him into the bathroom here. Say what?! While alien transporters have been seen in "Fallen Angel", "Tempus Fugit", and "The Red and the Black", it seems strange that peaceful aliens looking to meet humanity would lock the first human they meet into a locked bathroom, who could have starved to death in there for all they knew. Considering how Jose reacted though, he probably scared the crap out of them with all his screaming and yelling! They probably got spooked and waited for a mature human to come by! Then again, if these aliens were a Syndicate hoax (though that is highly improbale) getting rid of Jose would make sense.
Jose says the aliens are still out there in the woods. How would he know? He's been locked in a bathroom the past day!
The aliens seemed to have studied the Voyager signal, so that they repeated the welcome part on purpose in order to communicate with humanity. Notice how they repeatedly send signals, waiting for someone to arrive.
Did Jose really die of fear? Why the sudden rigor mortis then? Might he have been flashed with radiation from the UFO or from the aliens on purpose?
Could this Willowy Grey be a Rebel alien, trying to contact humanity to become an ally in their war with Purity, or maybe to warn them of the upcoming invasion and colonization? Remeber Colonists have been shown as Willowy Greys, so if this is true then Willowy Greys are not all Colonists it's just that some/most have been conquered by Purity and are not controlled.
Was this alien the one who sent the WOW signal?
Aliens in "Conduit" give a boy the Voyager signal in binary code. Was this the same aliens, making a little alien abduction to see what humanity is like and then readying for their first contact.
When the alien comes to meet Mulder, it hovers in its UFO just outside the door, sending a written signal. It then 'reads' Mulder's tape of his own voice, and trys to speak to Mulder by repeating his speech. If the alien knew what he was repeating, was he trying to warn Mulder/humanity to trust no one because it was trying to warn them about the Syndicate/Colonist Alliance?
So the alien uses his telekinesis to open the door to walk in to meet Mulder. His UFO is causing that wind to fly all over the place. He is confused when Mulder shuts the door, so he goes away for a second. Then he comes back again, opening the door again with telekinesis. But this time he must push equipment away and open a lock! How curious! So he walks in the door to meet Mulder, and finds him trying to shoot him! Fortunately guns can't fire near an operating UFO, so the alien leaves after somehow knocking out Mulder or erasing his memory of how he left.
Like the BlackOps team in "Paper Clip" this one fires at Mulder (and Scully) but its hard to tell whether they were trying to scare him off convincingly or really kill him. But they obviously let him go! As Deep Throat said last episode, "these men do not make mistakes". They let him go as per Cancer Man's orders, as part of Cancer Man's little project to return Mulder's faith. He does the same thing in "Redux II" when Mulder doesn't believe in aliens anymore, at least he tries to.
We never see in this episode Mulder's phone being tapped. Did Mulder just make this up? Did he just assume it was being tapped? Or at some point between seasons did he check his phone and find a tap on it?
This is the first time Cancer Man speaks to Mulder (or Scully for that matter). He appears very aggressive, but he is probaly just playing mean so Mulder doesn't realize their connection, and also to keep up the myth about HUMAN conspiracies and return Mulder's faith.
This was the first indication that Skinner wasn't a complete Syndicate stoodge, when he orders Cancer Man out of his office and protects Mulder from punishment. Of course, if Cancer Man really wanted Mulder gone he could do it (I think! In "The Beginning" he allies with Jeffery Spender in order to drum Mulder out of the FBI but maybe that was to work with his son or maybe after his 'death' the FBI didn't recognize him anymore). So Cancer Man is once again acting as a hard ass out for Mulder.
Was it just the natural side effects of the alien UFO that erased the tapes? Probably. Or maybe after this disappointing first contact the alien decided to forget humanity so it paralyzed Mulder, erased his memories of the visit, then erased all the evidense.

THE HOST

The Run Down:

Skinner puts Mulder on an unofficial X-File. Mulder at first protests, thinking it another punishment job.
Mulder later receives a phone call from someone (X) who says "you have a friend in the FBI" then hangs up.
Someone later covertly gives Mulder and Scully information on the unofficial X-File.
Skinner congradulates Mulder on the work, and says this should have been an X-File but "we all take our orders from someone".
X later calls Mulder again to say "success in your current assignment is impertitive...reinstatement of the X-Files must be undenyable".
Mulder later shares with Scully his phone calls.

Plot Points:

Skinner gives Mulder an unofficial X-File. He later says "we all take our orders from someone".
Mulder first meets X on the phone, who tells him he has a friend in the FBI, that success in this case is imperitive in order to reinstate the X-Files, that must happen.

Analysis:

X's statement that Mulder has a friend in the FBI could obviously mean Skinner, who as we first truely see in "The Blessing Way" is on Mulder's side and not Cancer Man's. BUT... this could also mean Cancer Man! He essentially has the FBI under his thumb, and maybe he wants the X-Files to be reinstated now so Mulder can continue his crusade. When Skinner reinstates the X-Files in "One Breath", Cancer Man could have easily countermanded it but he let it slide. So when Skinner says we all take our orders, maybe he means he was ordered by Cancer Man to give Mulder this unofficial X-File.
While we're at it, could X be working for Cancer Man towards this end as well? Most likely not; unlike with Deep Throat we definitely see that X is working against Cancer Man.

BLOOD

The Run Down:

Someone is experimenting on a town. Pesticides are sprayed over the town with stealth helicopters. The sprayed people then hallucinate that electronic LCD displays order them to committ murder. Mulder is similarly affected, but he is only ordered to leave town before the case is resolved.

Plot Points:

The government/Syndicate experiments on the unwitting American people with hallucinatory drugs which spurn normal people into violent behavior.

Analysis:

Similar tests occur in "Wetwired" where the drug/signal makes people see their worst fears, and the sign of the drug/signal activating is television static over vision. Again, electronic signals are involved. There is also the hallucinatory gas in "Unusual Suspects" which is later refined into a drug that makes people follow orders in "Three of a Kind".
Why exactly is the Syndicate intersted in this? Maybe its just the military with no Syndicate involvement. It's not very useful in either aiding or fighting the Colonists.

SLEEPLESS

The Run Down:

Mulder receives information on a mysterious killing from X. He shows the information to Skinner and tells him "my source, the only one I have ever trusted, is dead". Mulder is partnered with FBI Agent Alex Krychek because he opened the case just before Mulder asked for it and Skinner approved it. Krychek tries to befriend Mulder but Mulder tries to ditch him when possible.
The killer is part of a Vietnam era (1970) government experiment to create the perfect solider: these soliders can no longer sleep and the killer possesses the ability to psychically convince someone of a illusion so that it kills them. Now he is killing everyone involved in the project.
X calls Mulder for a meet: if anyone follows Mulder he won't show up. He has information on the case. He says Mulder can't contact him. He says closing the X-Files and seperating him from Scully was just the beginning. "The truth is still out there, but it's never been more dangerous. The man we both knew paid for that information with his life, a sacrifice I'm not willing to make".
Krychek kills the killer, who made an illusion that he had a gun. The information X gave Mulder was stolen by Krychek and Scully's office was ransacked to steal her copies. Mulder doesn't know if he can trust X.
Krychek reports to Cancer Man and three other men. Cancer Man asks where Mulder got the information. Krychek says either he's found a new source or a new source found him. Krychek recommends something in response. Cancer Man asks about Scully. Krychek says she is a problem, "a much larger problem than you described". Cancer Man says "every problem has a solution".

Plot Points:

Mulder meets Krychek for the first time: an FBI agent partnered with him but reporting to Cancer Man as a spy.
Mulder meets X in person the first time. X says he knew Deep Throat, that's why he does this, but he won't sacrifice himself.
Krychek tells Cancer Man that Mulder has a new informant and that Scully is a larger problem than he described. Cancer Man says that every problem has a solution, referring ominously to Scully.

Analysis:

This super solider experiment was before the '73 Syndicate-Colonist alliance, illustrating how before that alliance the Syndicate was desperetly trying to genetically engineer soliders/humanity to fight/survive the alien colonization. The Syndicate was using Vietnam as a testing ground for their latest experiments into the matter.
X tells Mulder that he won't be able to contact him, yet later in the season we see Mulder contacting X by taping an X onto his office window! What caused X to change his mind on this? It was a bad idea since this signal is what leads him into the Syndicate trap that kills him in "Herrenvolk".
X calls himself an associate of Deep Throat, yet as we later learn (especially in "Wetwired") he just a top lieutenant of Cancer Man responsible for the coverup situations as we've mainly seen. This would not seem to put X and Deep Throat together often in the working environment since Deep Throat runs the political coverups in D.C. while X is around the country. Maybe X reported to Deep Throat as he does to Cancer Man on his operations.
Were those three other men with Cancer Man Syndicate Elders? It seems unlikely they would concern themselves with such a matter.
Notice how Krychek volunteers ideas like that: that kind of over-eagreness, as he does with Mulder, shows that not only is he an FBI mole, but he is a Syndicate mole as well on behalf of the Russians as we later learn in "Terma".
Cancer Man is of course referring to abducting Scully and placing her in the Hybrid Program.

DUANE BARRY (part 1 of 2)

The Run Down:

June 3 1985: Duane Barry is abducted from his house by Lil' Greys. He screams "Not again!". Outside a circular UFO is hovering above his house, shining a bright white light down into it.
August 7 1994: Barry is in a mental hospital when he senses they are coming to take him to "the place". He takes his doctor hostage and escapes the hospital, only to get holed up with other hostages in a travel agency while looking for where the place actually was. Mulder (with Krychek tagging along) is called in for the hostage negotiations. Mulder befriends him over the phone.
At one the power fails and a bright light appears over head briefly. Barry shoots a hostage in terror and Mulder comes in with the med team. An electric transformer blew. Mulder is told to get Barry near a window so they can snipe his medulla oblongata (base of the neck). Mulder tells Barry the light caused a time loss, talks about alien abductios including his sister.
Barry reminses being paralyzed as he is levitated up. Later in the ship he is held to a table a lazer drills tiny holes in his teeth. The aliens speak telepathically. Barry says he sometimes sees young girls being tested. The government is in on it, they are even present sometimes watching. "They work together with a secret corporation... The government knows why they're here, but they wouldn't dare let the truth out. So they co-operate". The first place he was abducted was a moutain "ascending to the stars". He has implants, tracking devices, in his gums, nose, and belly button.
Mulder gets Scully to research Barry: he was in the FBI as of '82, been in and out of the nut house ever since. In 1982 he was shot in the head, with the bullet piercing the moral center of his brain, leaving him psychotic.
Mulder pisses off Barry, making him confused till he gets sniped. Barry survives. His FBI record was exemplory before he was shot with his own weapon in a drug stakeout and left for dead in the woods. Barry does indeed have implants and impossibly small holes drilled in his teeth. The implants have impossibly tiny barcode on them, and set a grochery store barcode scanner crazy. Scully asserts it was used "to catalouge him".
Barry awakes in the hospital suddenly, seeing light and Lil' Greys appear. He attacks his guard and escapes. Later Scully is in her apartment when Barry appears outside, breaking through a window and kidnapping her as she screams for Mulder's help on his answering machine.

Plot Points:

Enter Duane Barry: a repeated abductee of Lil' Greys and government agents who was an excellent FBI agent before being mysteriously shot with his own weapon in the head, destroying his sanity. He was shot and later abducted in 1982, but his first abduction occured at a mountain... ascending to the stars.
Barry's implants are tracking devices which have impossibly tiny barcodes used to catalouge him. He has implants in his gums, nose, and belly and impossibly tiny hoels drilled in his teeth.
According to Barry, the government is in on the alien abductions, they know why they're here but won't let the truth get out. They work with a secret corporation to co-operate with the aliens.
After a hostage situation Barry kidnapped Scully from her apartment.

Analysis:

Much of what Barry says could be false considering the brain damage he's had, yet most of it is supported with physical evidense.
Barry's August '82 abduction was not the first, suggesting he was being abducted before his gunshot in '82. Even after this abduction(s) he remained an excellent FBI agent. All this leads to suggest that Barry was a Fox Mulder without Congressional (and Cancer Man's) support to keep him alive, so he was abducted and later a frame-up shot him in the head with his own weapon to silence/discredit him.
Barry miraculously survives a gunshot to the head. Does he have some Hybrid blood in him to survive this, or was he just lucky? During the hostage situation the head sniper tells Mulder he needs to hit Barry in the base of the neck, which is the only place where various Hybrids and Pilots are vunerable. Was this just a coinicdense, or was Barry a very weak Hybrid with a low healing factor? If so, then the head sniper was a Syndicate man.
The teaser sequence has a date stamp on it and is not narrated, which pretty much makes it canon. The curious thing about it is the Circular UFO since Colonists use Triangular UFOs. The only non-Triangular UFOs ever seen were in "E.B.E.", "Paper Clip", and the Colonist Mothership in THE MOVIE so perhaps it's just a rare kind of ship.
We learn in "One Son" that the Colonists that the Syndicate made their alliance with took the form of Lil' Greys, so Barry appears to have abducted by real Colonists here. But the Syndicate is in charge of abductions, why would the Colonists waste their time with this guy? Perhaps this was a human abduction with a hypnosis to make him think it was aliens.
This abduction shows aliens who can paralyze, speak telepathically, and either they or their ship has telekinesis and maybe even transporation. These are all common features of Colonists.
The power failure and bright light were an obvious Syndicate attempt to set off Barry. They blow out a power station (or it was just the side effect of the UFO flying by) then buzz the site with a UFO, flashing their headlights so to speak so Barry would freak out.
Barry's Implants are different from the normal established Syndicate Implants, which don't appear until "The Blessing Way". Plus, these implants look like little metal scrap with tiny barcodes, not the Implants seen later which have tech in them. Is this a continuity error, or was Barry purposely given false crap because he was being set up as a patsy...see below.
Again with the teeth drilling... why? What's the point of this? It never again appears in the series.
In a throw-away line, Barry explains the entire Conspriacy! He says the governemnt and a secret corporation (the Syndicate!) work with the aliens because they know why they're here (Colonize the planet!) and don't dare let the truth get out, so they co-operate.
Yes, this entire Barry affair seems a Cancer Man setup to remove Scully as promised last episode! Barry has false implants and such because he was a pasty in waiting, something to produce if necessary rather than the real thing. So... Cancer Man broadcasts the summoning sense to Barry, who then escapes the hospital. He sends a UFO to buzz the hostage site so that Barry would get shot and in a hospital under minimum guard. Once there, he is given the summoning again and escapes with the superhuman strength he has a very weak Hybrid. He later meets Krychek, who tells him where Scully lives. Krychek probably even drove him there. If he grabs Scully, she will get abducted instead of him and they will all be happy... except for Scully that is.

ASCENSION (part 2 of 2)

The Run Down:

Mulder arrives at Scully's aparment, now a crime scene. Mrs Scully arrives as well, claiming she had a dream of "Dana being taken away". She says Dana doesn't believe in these things.
An FBI meeting on the abduction: Mulder, Krychek, Skinner, the Office of Professional Conduct Board members, and Cancer Man sitting off in a corner. Barry has disapeered with Scully in her car. Mulder is taken off the case by Skinner, but he figures out Barry is taking Scully to Skyland Mountain in Virginia. Krychek calls Cancer Man to say Mulder thinks she's been taken to Skyland Mountain, that he'll hold off Mulder "until they locate her". Mulder takes Krychek with him.
At Skyland Mountain Mulder takes a tramcar up the slope to beat Barry there, but Krychek cold-cocks the tram operator and turns off the tramcar. Krychek calls again to say he's got Mulder stalled, he'll hold "until you advise". Mulder tries to disembark the tramcar just as Krychek turns it back on. Mulder reaches the summit to find Barry alone and victorious as a bright light speeds off. Barry says that "they" took her as a stealth helicopter appears and spotlights them, spooking Barry.
Mulder interrogates Barry; he made a deal, her instead of him. His face has light radiation burns from the ship, but Mulder says he only saw a helicopter. Barry sees Krychek with two suited men, and warns Mulder, but he only sees Krychek outside. Barry says "They'll tell you where she is! The military's in on it just ask them!". Krychek is left alone with Barry for a moment before Skinner arrives. Barry soon dies mysteriously.
Somewhere, Scully is on an operating table. Grids of light play across her arms. A tube is attached to her stomach, and is inflating it as a drill approaches her from the cieling. Two obscured figures watch her.
Krychek meets with Cancer Man, asking what he should tell Skinner. Cancer Man says tell Mulder's version of the truth, "You've earned his trust, the object now is to preserve it". Krychek asks "For how much longer?", Cancer Man says "Until your assignment is complete". Krychek asks why not just kill Mulder he's such a threat, Cancer Man says "That's not policy. Kill Mulder and you risk turning one man's religion into a crusade." Krychek asks about Scully, Cancer Man says "We've taken care of that". Krychek asks how, he's got a right to know. Cancer Man replies "We tell you only what you need to know. You have no rights, only orders to be carried out. If you have a problem with that, we'll make other arrangements".
The Navy is handling Barry's autopsy and refuses to share their findings with Mulder. Mulder reports to Skinner, OPC, and Cancer Man saying he didn't kill Barry, he was poisoned and the military covered up the toxicology report because they know where Scully is.
Mulder goes to see Senator Matheson but is intercepted by X, saying Matheson can do nothing "without committing political suicide. They have something on everyone, the question is when they'll use it. No one can help you now. Your channels of appeal and recourse are closed". Mulder says Deep Throat could have helped me, and asserts X knows what's happened to her. X only says "This reaches beyond any of us, even my predecessor. There are no answers for you. They have only one policy, deny everything".
Mulder finds cigarette butts in Krychek's car, and asserts to Skinner that Krychek was in on it. The tram operator disappeared and was later found dead. Mulder also implicates Cancer Man. Skinner mentions about Krychek saying "I didn't give him the assignment, I only-". Krychek has disapeered. Mulder is pissed but Skinner re-opens the X-Files, because that is what they are afraid of.
Mulder meets with Mrs Scully, and gives her Scully's cross but she tells him to keep it. She continues to have the dream about Dana being taken, and Mulder says that it's only bad when it stops.

Plot Points:

Scully's mother is psychic and had premonitional dreams about Dana's abduction.
Krychek, under Cancer Man's orders, stalls Mulder so that Barry has time to take Scully to Skyland Mountain, where he was first abducted. Something with a bright light and emitting radiation takes Scully, later when Mulder arrives a stealth copter is watching them.
According to Barry, the military is in on the abductions.
Krychek poisons Barry, killing him. Mulder discovers Krychek's duplicity and Krychek promptly disapeers.
X tells Mulder that "they" have something on everyone, including Senator Matheson. He says Scully's abduction is beyond all of them, even Deep Throat. He says they have one policy: Deny Everything.
Skinner re-opens the X-Files because that is what "they" are afraid of.

Analysis:

Scully and her mother are psychic! Scully's psychic abilites were shown in "Beyond the Sea" and later in "The Blessing Way". This is very ironic, suggesting the reason Scully is such a skeptic because she is in unconsious denial about her extrasensory abilities.
This is the first appearance of the OPC Board, though they are not named as such but later referred to in this episode.
Krychek is to stall Mulder until they find her. This suggests that the Syndicate/military doesn't know where Barry is heading, despite the fact that Barry has said he would go to his first abduction. Doesn't the Syndicate know where he was first abducted?! Or are they worried that he'll go somewhere else in his crazed state? Perhaps by coincidense the Colonists abducted him first, and the Syndicate did the later abductions. Or maybe this is an inconsistancy as the episode suggests it was really aliens but we later learn the Syndicate abducted her in various episodes, unless the Colonists took her and gave her to the Syndicate, as they did with Cassandra. In any case Scully was taken by a UFO because Barry had radiation burns.
Why did a stealth copter come by later and flash Mulder and Barry? To check up on them? If aliens did abduct Scully then the Syndicate wanted to make sure she was taken. Maybe it was just to spook Barry.
Barry seems to think that the military will tell Mulder where Scully is if he asks them. What...?! Surely he's deluded here!
What's happening to Scully? While the light grid on the arms thing has never been explained, she was being injected with alien sperm/hormones into her uterus, preparing her to birth an alien-human Hybrid. As for the drill, who knows? The only implant she has is in the back of her neck, and she is face up on the table.
The two figures watching her are human, most likely the Japanese Axis scientists overseeing the Hybrid program. Though of course in "Two Fathers" we learn that Cancer Man and Openshaw were heading the Hybrid Program.
Krychek was assigned to Mulder in the hopes of gaining and keeping his trust, so Cancer Man knows what he's doing at all times.
Cancer Man tells Krychek that killing Mulder is not policy because he would matryr the believers' cause. While this is true, in actuality Mulder lives because Cancer Man sees him as his pseudo-son and the son of his friend Bill Mulder but Cancer Man keeps this secret from everyone else.
Krychek displays his true colors when he tries weasel out information on Scully's abduction from Cancer Man, saying he has a right to know. Cancer Man shoots him down, saying he has no rights and if he feels otherwise they'll make other arrangements (read: he will kill Krychek). As we learn in "Terma", Krychek is a mole from the Russian Syndicate sent to learn information on the Syndicate's progress on the Vaccine to the Black Cancer.
So Matheson is being blackmailed into non-action by the Syndicate. This of course puts his actions in "Little Green Men" in a suspicious light, as well as his appearance in "Nisei" and his appearance in "S.R. 819" where he is actively shown to be a pawn of the Syndicate.
X tells Mulder the Syndicate has something on everyone, showing they can blackmail their way through anything.
X says Scully's abduction goes beyond him, Mulder, and Deep Throat. Surely he's speaking not in the context of knowledge but in philosophical terms, that alien colonization is beyond all of them.
Mulder seems to make a big leap of logic from cigarettes in Krychek's car to Krychek and Cancer Man being behind Scully's abduction. Remember he saw Cancer Man in "Young at Heart" as a dirty CIA man and Cancer Man was chewing him out in "Little Green Men", so I guess he just put two and two together.
Skinner begins to mention he didn't assign to Krychek to Mulder, he only-. This suggests that Cancer Man forced Krychek on Skinner, saying to have him assigned to Mulder.
Skinner obviously couldn't re-open the X-Files if Cancer Man didn't want it, so Cancer Man wants it. Why?

ONE BREATH

The Run Down:

Scully mysteriously appears comatose in a D.C. hospital with no signs of injury. According to her living will she must be taken off of life support. Mulder meets Missy Scully, Scully's new age sister who claims to sense Scully's soul trying to decide whether to move on or stay. Mulder signals for X on his window but X does not appear. A mysterious Nurse Owens speaks to Scully and she can hear her. Scully is taken off life support but does not die.
Mulder has the Lone Gunmen examine Scully. Her blood has "abnormal protein chains" whose amino acid sequence is in an unknown combination. These protein chain are the result of branched DNA, according the newest Lone Gunman The Thinker, who they only meet on the internet. They call branched DNA the cutting edge of genetic engineering, the biological equivilant of a microchi, tech which is 50 years away. It could be used as a tracking system, a biological marker, even grafting a human into something inhuman. But the branched DNA is inactive, a waste product. The experiment is finished, and now it's just a biological poison which will kill her.
A nurse takes Scully's blood just as a woman Overcoat Man was standing by has a heart failure. Overcoat Man steals the blood sample and flees, with Mulder chasing after him. Mulder chases him into the parking garage, where he is intercepted by a very nervous and armed X. X says he didn't expect Mulder to arrive until later, says to forget Overcoat Man and demands he forget about the men who abducted Scully. X says Mulder has gotten Deep Throat and Scully killed, but that's going to happen to him. "You are my tool, do you understand? I come to you when I need you. You're heading them in a direction that can lead them right here". X says Scully is as good as dead, he should mourn her and walk away. X says "I used to be you. I was where you are now. But you're not me. I don't think you have the heart. Walk away... you will be able to live with yourself, until the day you die".
Mulder breaks free and chases after Overcoat Man while X must stay in the shadows. He catches him after a gunfight. Overcoat Man gets the drop on Mulder though, but X executes Overcoat Man saying this is what is needed to find the truth. He agrees "to attend to this" for Mulder.
Cancer Man tells Skinner about Overcoat Man's death at the hands of Mulder, and says "If you're having trouble sitting on Mudler... I'm sure you know we'd have no trouble". Skinner grills Mulder about it, who feigns igonorance. There is no body. Mulder wants to know where Cancer Man is, he's behind all this. Skinner asks if he'll kill him for justice. Mulder blames himself for never telling her about the risks involved in his investigations.
An FBI woman gives Mulder a Morley's cigarette pack with Cancer Man's address: 900 W. Georgia St. Mulder storms Cancer Man's simple apartment and holds him at gunpoint. Cancer Man asks how he found him. He claims to have "watched presidents die". He says "I like you. I like her too. That's why she was returned to you". Cancer Man says he has no wife, no kids, some power. "I'm in the game because I believe what I'm doing is right... If people were to know the things I know, it would all fall apart". He told Skinner that Mulder was the one who killed Overcoat Man but he didn't believe it until know. "I have more respect for you, Mulder. You're becoming a player. You can kill me now, but you'll never know the truth. And that's why I'll win. Don't worry. This'll be our secret. We wouldn't others to start rumors". Mulder leaves disgusted with himself.
Mulder types up his resignation but Skinner refuses it. Mulder says he hates what he's become. Skinner tells how he went to 'Nam as a teenager, and lost faith in everything. His entire squad was ambushed and killed, but he had an out of body experience and survived. He is afraid to look beyond that event, but Mulder isn't and that's why he must continue. Skinner gave him Cancer Man's address.
X meets Mulder again with a plane ticket. X says "I can't tell you why she was taken. It's too close to me", but he's giving him the men who took her. They will think Mulder is out of town and information on Scully in his house, they come at a specific time to search his apartment, where Mulder will be waiting armed to defend himself "with terminal intensity". It's the only way, "The law will not punish these people". After this, they cannot make contact for several weeks. Mulder is waiting in his apartment, but after speaking with Missy who says Scully could go any time now he instead spends the night at Scully's bedside while the men ransack his apartment.
The next day Scully awakens from her coma. She doesn't remember anything about her abduction. Mulder gives her back her cross, she says she had the strength of his beliefs. She asks about Nurse Owens, but there is no Nurse Owens at this hospital.

Plot Points:

Scully is mysteriously returned comatose to a hosptial.
Mulder contacts X by taping an X onto his apartment window and waiting for the signal.
Her blood has strange protein strains because of now inactive branched DNA that was used to experiment on her but is now killing her. The branched DNA is 50 years away and could be used to catalogue or graft human into inhuman.
A man tries to steal Scully's blood but gets executed by X.
Skinner gives Mulder Cancer Man's apartment number. Mulder threatens Cancer Man who claims to have watched presidents die, he believes he is doing the right thing because if people were to know what he knows it would all fall apart.
Mulder tries to resign but Skinner refuses.
Skinner had a near-death experience in Vietnam.
X says Scully's abduction is too close to him for him to tell Mulder about it.
Scully awakens from her coma after being cared by a mysterious Nurse Owens who disapeers.

Analysis:

Presumably after Scully birthed her Hybrid, Cancer Man had her shipped to the hospital because he wanted her returned to Mulder. But what about her being on the brink of death? Consider this: Scully encounters a group of fellow female abductees, and they all survived this killer protein strain! So either Cancer Man knew that this problem just cures itself eventually, or (and this is stretching it) Nurse Owens was some kind of Syndicate plant to 'cure' Scully through metaphysical means. Or maybe they just injected her with something.
So Scully was injected with alien protein strains, but the Lone Gunmen say these are from branched DNA the futuristic equilvilant of a tracking device. Little do they realize this is alien bio-technology! They also mention it could graft a human into an inhuman, and this seems to be what it really did: Scully was given this to make her body ready to birth a Hybrid, then she is given the alien sperm/hormones which creates the Hybrid fetus. The alien protein strains make her body capable of this. The branched DNA might also have the purpose of catalouging her, but we learn in "Herrenvolk" that this biological marker is on the smallpox enoculation scar and not just running around in the bloodstream.
So X and his lower-influence partner come to the hospital to steal Scully's blood sample, so the Syndicate can check on her progress in surviving the branched DNA. X sends Overcoat Man to steal the blood while he waits in the garage for him. Unfortunately Overcoat Man returns with Mulder on his tail, so X grabs Mulder into the shadows and stalls him while he hopes his partner gets away. He didn't think Mulder would be here at this time! Yet while they're talking Overcoat Man is still nearby, so he appeared to be watching X and Mulder argue. Mulder then chases after Overcoat Man again, X follows and executes Overcoat Man because he saw X and Mulder together talking.
X says he used to be where Mulder is now, trying to choose between becoming a "player" or holding morals. Does this mean X used to be an FBI Agent with a partner dying, or is it the more general sense of deciding whether to work for the Syndicate or not?
X also explains to Mulder that he comes to him, not the other way around. Yet in this episode they have a system where Mulder can contact X! When did they work this out, and if X never wants to be contacted by Mulder why did he agree to this?
Overcoat Man's body disapeered yet Cancer Man knew about his murder... and the hands of Mulder. This shows that X took the body and then told his superior Cancer Man that Mulder shot him! The first X-Cancer Man connection!
HAS Cancer Man watched Presidents die? The obvious canidate is JFK, and we see Cancer Man killing JFK in "Musings of Cancer Man" which is almost definetly a ficiticious story. This was more likely just a bluff.
Cancer Man lies to Mulder several times. He says he has no wife and no kids: Cassandra and Jeffery Spender are his wife and son! He says he has some power: he is one of the most powerful men in the world!
X considers Scully's abduction too close to him to tell Mulder about it. This suggests that X was directly invovled in her abduction, and thus Mulder wouldn't trust X anymore.
The men who ransack Mulder's apartment are obviously not the same person who took Scully, they are just some Cancer Man cleanup men while the military took Scully.
So who was Nurse Owens? Most likely some kind of angel.

RED MUSEUM

The Run Down:

A Wisconsin boy named Kane is found in the forest scared and in his underwear with the words "He is One" written on his back. He claims to have been possessed by a spirit. The bathroom of his house has a hidden room where someone watches. There are similar cases in nearby cities. In the vicinity is the Church of the Red Museum, a spiritual reincarnation/vegetarian cult who channels dead spirits which tell them a new kingdom begins in 18 years. A girl is taken by a man with a cloth over her mouth; later she is in her underwear in the forest, hallucinating animal attacks. Her back has "She is One" written on it. The girl had "an unspecified alkaloid substance" in her blood, as well as a powerful hallucinogenic used by kidnappers to subdue their victims. It is a controlled substance so only a doctor could get it. The Red Museum leader was a doctor fired for unethical practices but says he never handled the hallucinogenic.
An old man shows Mulder and Scully two men injecting cattle with genetically-engineered growth hormones. He thinks it this government approved hormone that is making the townsfolk more aggressive the past few years. One of the two men, Thomas, is the man who peeped in the house. A plane crash kills Dr. Larson, the doctor who has treated all of the abducted kids and was tracking their families through credit cards. He would give children vitamin shots,and they never got sick. Kane's father objected, and died in an accident. On his body were vials of something and cash. Mulder and Scully discover the hidden room in the Kane house. A video camera and hundreds of video tapes.
Crew-Cut Man arrives and executes Thomas' associate. Thomas abducts another boy, but this boy is found dead and Thomas is implicated and arrested. Crew-Cut Man is on the scene, and Scully recognizes him. Thomas tells Mulder he abducted them and wrote on their backs, but never killed anyone. He confesses being a pervert, but he did it because they had become monsters from Larsen's tests. Larsen paid him to innoculate the cattle with it. Scully finds that Larsen's vials had Purity Control in them: "synthetic corticosteroids with unidentified amino acids". Mulder asserts the kids have been injected with alien DNA to see how their bodies would react. Scully tells Mulder the man who killed Deep Throat is the one killing the operatives here.
Mulder thinks Crew-Cut Man is out to kill any children innoculate so they are hidden with the Red Museum cult. Mulder tracks down Crew-Cut Man in a slaughter house which he is trying to torch. Crew-Cut Man knocks out Mulder but Scully and police arrive, killing Crew-Cut Man. The body of Crew-Cut Man cannot be identified. Larsen's vials were further analyzed and were broken down but found to be unrecognizable. The kids are now devealoping severe flu-like symptoms. Scully thinks the Red Museum was the control group in the testing.

Plot Points:

Crew-Cut Man is dead, killed during a clean up operation involving the innoculation of children with Purity Control.
The Syndicate has been injecting children with Purity Control; it has made them aggressive but immune to sickness. When the regular innoculations ended, the children devealoped severe flu-like symptoms.

Analysis:

The Red Museum thinks a new kingdom begins in 18 years. 1994+18=2012. The Syndicate says that the Colonist Invasion is supposed to occur 15 years from 1998. 1998+15=2013. Is this a coincidense?
Deep Throat claimed in "The Erlenmeyer Flask" that cloned DNA from the alien fetus was innoculated into children in a southern state. That mirrors this episode, so it can be assumed that this experiment happens elsewhere and is continuing.
Since Crew-Cut Man was involved, Cancer Man was involved. Considering the importance of anything related to the alien fetus, that's not very surprizing.
Why does the innoculation make the subjects aggressive? Does this mean that other Hybrids would be vicious, or is this a primitive test not connected with the Hybrid Program?
The children were injected with a growth hormone laced with "unidentified amino acids", which Scully immeadiate concludes to be Purity Control DNA. So are any unidentifyable amino acids by definition alien?
Was Crew-Cut Man really going to try and kill all the innoculated children?
Why were the innoculated chilren devealoping a severe flu after a lifetime immune to sickness? Presumably it was because they were no longer receiving the innoculations. Will these children now die?
Crew-Cut Man's body was unidentifyable. This trend in Cancer Man assassins continues with Luis Cardinal and others.

FRESH BONES

The Run Down:

X contacts Mulder for a meet. He offers information on a case Mulder is working about a military/government coverup for revenge against a Hati voodoo curse. Mulder is suprized to see him, he says "I had assumed our last contact would be our last".

Plot Points:

X returns to Mulder, who thought their relationship was over.

Analysis:

Mulder thought their relationship was over because of "One Breath" where Mulder pretty much saw X was directly working with Cancer Man and all the other men responisble for Scully's abduction. X said that after helping Mulder, they couldn't have contact for a few weeks. How did Mulder infer from that that they would end their relationship?
Maybe X has come back to Mulder because he truely does need Mulder. He was hoping to wait for Mulder to be the one asking for him, but neccessity made him take the inferior position.

COLONY (part 1 of 2)

The Run Down:

In the sea in the Artic Circle, a merchant boat is being followed by a UFO after eariler passing over them quickly. It flies by them again, crashing into the sea. They go to investigate and rescue what is believed to be a Russian fighter pilot who miraculously survived the cold. This Pilot was brought to an Alaska hospital then walked out and disapeered.
In a Pennsylvania abortion center, a Dr. Prince is alarmed to see the Pilot's face on a news report. He flees but is caught by The Pilot, who asks "Where is he?". Prince says he doesn't know, and the Pilot holds him down to the ground and takes out a metal cylinder which shoots out a icepick-like blade. This is called a Glimlet. He stabs Prince in the back of the neck, and a bubbling green liquid boils out. The Pilot starts a fire and leaves. Two other identical abortion clinic fires killed two other identical doctors.
These 3 obituaries are e-mailed to Mulder by someone. No record exists on the three Gregors, and no remains are discovered. A mysterious man placed articles asking for information regarding a picture of a Gregor. Mulder and Scully use the article responses to track the nearest Gregor in Syracuse New York.
Mulder sends Agent Weiss to protect the Syracuse Gregor. The Pilot finds this Gregor who argues with him. The Gregor says "There were years, years when our people did get along, where we could share the entire planet. But you seem to be unwilling to share. I don't understand, you did not fail...". The Pilot responds "Your plans will not succeed" and kills the Gregor. Weiss breaks in and shoots the Pilot in the chest. The Pilot is not injured but the same bubbling green blood boils out. Weiss becomes infected through the eyes and falls down in pain. Later Mulder and Scully arrive to see 'Weiss' who tells them the Gregor isn't there. 'Weiss' has Weiss dead in his trunk, with his eyes nose and mouth inflammed. 'Weiss' morphs into the Pilot.
Mulder is called into DC by Skinner. Skinner asks why he was working without official approval, Mulder thought they had an understanding concerning the X-Files. Skinner says it is because Weiss is dead, and he is off the case. Mulder and Scully both get an e-mail locating the next Gregor in DC. Mulder goes to Scully's apartment where he meets 'CIA Agent Chapel' who tells them they are Russian clones called Gregor, smuggled into America as doctors to sabotage the medical infrastructure during a war. They began to arrive in the mid '70s. Now the US is allowing a Russian spy killer to quietly take them out, and 'Chapel' wants to help them expose the truth. 'Chapel' placed the article. The DC Gregor works in a large warehouse with four large green tanks, he drives off with a Samantha. When Mulder, Scully, and 'Chapel' arrive the DC Gregor has Samantha hide and he jumps four stories when he sees 'Chapel'. They chase the Gregor, who is eventually cornered by 'Chapel' and killed. Scully comes across the bubbling green puddle that is all that is left of Gregor, which eats through her shoe. 'Chapel' claims he escaped. Scully doubts 'Chapel' but his CIA record is legitimate, a 17 year career. Weiss' body has no toxins in it but enormous red blood cell production coagulated the blood.
Mulder is told by Skinner that his father Bill has been calling, there is a family emergency. Mulder calls Bill's house and is surprized when his mother Teena picks up. Bill says he received a very strange phone call, and will know more when Fox gets there. His sister Samantha is there! Teena questions Fox if it really is her. Samantha says she was nine or ten when she was returned amnesiac, and placed with a family who raised her. She recently underwent hypo-regression therapy and began to remember her family, the abductions, the tests. She says her life is danger by the man who is hunting her father and the other doctors. She calls them "my adoptive parents. They're only visitors here- what people would call aliens. A bounty hunter's been sent to kill them.... He won't stop until he's killed them all and anyone who tries to stop him. He'll come for me soon". She says Mulder has met this man. Mulder calls Scully to warn her but misses her. Samantha says "she may not be able to recognize him, he has the ability to disguise himself... You can't recognize him, but I can".
Scully tracks down the Gregor warehouse, and witnesses 'Chapel' destroying all the equipment there and the 4 green tanks. She is followed to her apartment. She moves to a motel, followed by the Pilot. She returns to the warehouse, finding a small moving alien fetus in one of the destroyed bags and the last 4 Gregors. They say they cannot harm her, and she must protect them. She has them placed in a maximum security prison, observed by the Pilot. The Pilot, disguised as a warden, enters the prison and kills the last Gregors. Scully meets 'Mulder' at her motel room, just as Mulder calls her up on the phone...
Later, Mulder is brought to a medical facility by a military helicopter. He is weak and suffering from hypothermia. Scully arrives and tells the doctor that raising his body temperature will kill him. The doctor wants to warm him. Mulder narrates that his faith is based on his belief in Samantha's abduction, and that after what happened on the ice he would be ready to die because his faith has been confirmed. He knows "that there is intelligent life in the universe other than our own, that they are here among us, and that they have begun to colonize".

Plot Points:

Enter The Pilot: an alien bounty hunter who has super strength, can morph his apperance, and has the alien retrovirus in his blood which is leathal for humans. In this appearance he is killing Hybrid clones who have set up an illegal colony using Samantha Hybrid clones. Hybrids can see through his disguises somehow.
Enter The Glimlet: the alien blade used to kill Hybrid clones by the Pilot. It is a metal cylinder, which on activation extends an ice pick like blade which is used to stab the Hybrid in the back of the neck.
A small group of identical Hybrid clones are setting up a small colony on Earth along with grown Samantha Hybrid clones. They work in abortion clinics and are experimenting with alien fetuses in green tanks.
The Pilot's people and the Gregor's people used to get along and think they could share Earth, but lately the Pilot's people have gotten greedy and want the planet for themselves. The Pilot says their plan will not succeed.
When a Hybrid is stabbed in the neck with a Glimlet, it bleeds a bubbling green blood and decomposes into an acidic puddle of bubbling green goo. This presumably also releases the alien retrovirus.
Humans die to the alien retrovirus because their blood clots, coagulates through overproduction of red blood cells.
A Samantha Hybrid visits Mulder's divorced parents, Bill and Teena Mulder. They doubt if she's the real thing.
Mulder has seen proof in exterrestial life, and knows they have begun to colonize.

Analysis:

The actions of the Pilot's UFO are very suspicious. It buzzes a merchant vessal, then follows it for awhile before buzzing it again, this time crashing it into the sea. Was this on purpose, and if so, why?
If the Pilot crashed it on purpose, it would be to be recovered by the ship in the guise of a Russian pilot, thus covering the fact that he is an alien. It would explain his interest in the merchant ship. But is this necessary? He obviously knows the Gregors are in the US, as he goes there immediately and then sets up the article to learn the locations of the Gregors in Northeast US. So this Pilot can speak English, has everyday knowledge about life in America including how to drive a car and place an ad. Given all this, was it neccessary to crash land in the Artic? Why not land in the US? Is it because of the electronic fence protecting the US, mentioned in "Fallen Angel"? Did he crash so that his UFO would be in a safe place for when he left, even though he would have to get back up to the Artic somehow?
If the Pilot didn't crash on purpose, why did he crash?
In "The Red and the Black", we see a Rebel Pilot UFO has a crew of three Pilots. It stands to reason that this UFO would require three Pilots, so were the other two Pilots sitting in the UFO this whole time?
The Pilot is after someone in particular, not just Gregor Hybrid clones. See "End Game".
There is no reported sign of the Hybrid puddles at the crime scenes, so it stands to reason that this puddle literally boils away into gas, leaving no physical sign of the death.
How do the Pilot and the Gregors fit into what we now know about the Colonists and the Pilots? The Gregors are Hybrids but cannot morph, the same goes for the Samanthas, but Hybrids are always shown to working for the Colonists (except for the rebels in "Memento Mori" who do the same things as the Gregors do). The Pilots are shown to either be Colonist soldiers, or rebels against the Colonists whose faces are sealed to prevent Purity infection. So presumably this Pilot is Colonist-loyal and the Gregors are rebels from the Syndicate Hybrid cloning programs, just like the Kurt rebels in "Memento Mori". The Syndicate has called in a Pilot because the situation is out of their control. Yet one Gregor says to the Pilot that there was a time when their two peoples would share the Earth but now the Pilot's people are greedy. What...? This dialogue actually only appears in closed captioning so maybe it is non-canon. It would not seem to make sense unless the rebelling factions have recently openly split after long arguing about what to do with Earth.
It is never actually shown that these Hybrids will release the alien retrovirus, but the Pilot does and the Weak Hybrids in "The Ernlenmeyer Flask" did so presumably these do as well, the green blood being the visual indicator.
This Gregor also says "I don't understand, you did not fail...". What does this mean? It seems to suggest that if the Pilot's people did not fail in whatever they are talking about then hunting down the Gregors would not be neccessary. Does this refer to Colonization?
The Pilot knows where Scully lives and that Mulder is heading over there. This suggests surveillance on Mulder and Scully their phone lines, again suggesting that the Pilot is in contact with Cancer Man and the Syndicate.
'Agent Chapel''s story is obviously fluff but notice he says the Gregors entered America in the mid '70s, which is when the Syndicate formed its official alliance with the Colonists.
Where did the Gregors get that mini alien fetus? Was it cloned from themselves or stolen from the Syndicate?
An autopsy on a human killed by the alien retrovirus shows no toxins in the system.
Bill Mulder tells Fox he got a strange call, and later Samantha appears. Was it Samantha who called?
Notice Teena Mulder's skepticism that Samantha is real. Does she know about Hybrids and clones and such?
Samantha's story to Mulder is also most likely fluff.
Why does Samantha call the Pilot a bounty hunter? This suggests he is not alligned with any nation just working for money. Maybe this was what he was going to be in Cris Carter's mind only to be changed later, or maybe this was another lie by Samantha. Why would she lie? To keep the secret of what the Gregors were doing or who they're associated with from Mulder?
How can Hybrids see a Pilot through his disguise? Some telepathic or other extrasensory perception?
Scully sees the Pilot at the warehouse destroying it, then later returns to find the last 4 Gregors. Were they there when the Pilot was there, or had they just arrived like Scully?
How did the military know where to find Mulder? See "End Game".
Why does Scully say warming Mulder will kill him? See "End Game".

END GAME (part 2 of 2)

The Run Down:

A US naval sub is crusing the Artic sea when it encounters a UFO sitting under the ice, 80 feet across and emitting random radio noise with no pattern. The captain consults with his peers and is ordered to torpedo the craft. They approach the craft and lock torpedoes; electronic systems short out and the nuclear reactor dies. The captain orders to surface the sub through the ice.
Scully pulls a gun on 'Mulder' who easily dispatches her, asking "where is he?" before leaving with Scully.
Mulder and Samantha later arrive, and Samantha knows the Pilot was there. She says Scully was taken to make a trade for her. Mulder asks why he wants to kill her, she says "because I know how to kill him. By piercing the base of his skull, this is the only way to kill him and it must be precise. I'm fairly sure it will work. He's got powers I've never seen before. If it doesn't work, there's a chance you'll die. Their blood is toxic, human exposure to it is fatal". Samantha talks about her foster parents: "the progeny of two original visitors, clones who have been attempting to establish a colony here since the late 1940's. The community, by necessity, is dispersed. There are clones identical to my parents living [across the country]. It's their belief that our stewardship of the planet is being forsaken... they'll someday become the natural heirs. Through hybridization, they've been working to erase... their identical natures. [They work in abortion clinics for] access to fetal tissue. Though the biologies are incompatible, they finally found a way to combine human DNA with alien DNA. The experiments weren't sanctioned. It was considered a dilution of their species, a pollution of their race. So a bounty hunter was dispatched to destroy them and terminate the colony".
Skinner visits Mulder, Samantha senses it isn't the Pilot. Scully calls for the Pilot to tell where the trade will happen. Mulder asks for Skinner's help and trust. The switch happens at a bridge, with Skinner and a sniper waiting for a shot. Samantha tries to attack the Pilot with an icepick but he disarms her, saying "tell me where she is". The sniper shoots the base of the Pilot's neck, and both the Pilot and Samantha go off into the river. The river is searched but the Pilot's body is never found. Mulder told Skinner the Pilot was an alien. Later Samantha's body is recovered. As it warms from the river, it decomposes into a bubbling green goo.
Mulder tells his father Bill, who is immeadiately suspicious about the Pilot, asking "was this your decision?". Samantha left an address with Bill for Mulder in case they ever became seperated; another abortion clinic. Mulder goes there and finds 3 Samantha clones and more green tanks. They say they knew he could be manipulated, 'she' must be dead, they must flee. They tell Mulder they are dispensable, a 4th Samantha appears who they say "was the first. The one from which we all came. The one you must save". The 4th Samantha tells him "we know where your sister is, how else would we know so much about her?". The Pilot arrives and the Samanthas flee. Mulder goes after the Pilot but is quickly knocked out. A fire starts, and later Mulder is the only person found by firemen.
Scully examines Weiss' blood. There are blue retroviruses which triggered the massive red blood cell production. When the retrovirus' temperature is lowered 5 degrees it goes completely dormant.
Mulder meets X, he wants to know what X knows. X says "they're all dead. A nuclear sub located [The Pilot's] craft... they were ordered to destroy it but they were disabled. An attack fleet left port... to make sure this man does not leave. You'll only win the war if you pick the right battles. This is a battle you can't win". X leaves.
Mulder quickly disapeers off the face of the earth, leaving a warning with Scully not to follow him. Scully asks Skinner to help her locate Mulder "through unofficial channels". Skinner refuses. Scully signals for X at Mulder's apartment. When X sees Scully at the door he pretends it was a wrong number and leaves. He is intercepted by Skinner, who asks if he told her what she needs to know. X pulls his gun but Skinner fights X in the elevator for awhile. X gets the drop on Skinner, saying "I've killed men for far less" but Skinner says he'll be killing two men. Skinner later appears to Scully beaten, with the exact co-ordinates of Mulder's destination.
In the Artic ice fields, Mulder reaches the surfaced abandoned submarine. Mulder finds a 'crewman' who claims after they surfaced a man came and locked half of the crew away without air then executed the rest. He says all the other crew are dead. Mulder handcuffs the 'crewman' and holds his gun at the base of his neck, saying "you're not getting back to your ship until I get the truth", and demands to know where Samantha is. Mulder says if he tells him he'll let him get back to his ship before it's destroyed. The Pilot morphs to his true form and bangs around Mulder, who continues to ask where she is. He says "if I wanted to, I could have killed you many times before". He finally says "she is alive". Mulder shoots the Pilot and gets infected. The Pilot drags Mulder outside and commands the submarine, submerging it and nearly killing Mulder.
Scully is able to convince the Navy doctor not to warm Mulder. "Transfusions and aggressive treatment with anti-viral agents" have slowly cured Mulder. No trace was found of the submarine or the Pilot. Mulder was found by a Naval recon squad and choppered to the Navy hospital. Mulder tells Scully he's found the faith to keep looking.

Plot Points:

The Pilot's UFO is 80 feet across, and emits a wide array of electronic noises. It can disable the electronic systems on a submarine and can emit some kind of sound weapon all while the Pilot was not on board.
According to Samantha, the only way to kill the Pilot is to pierce the base of his neck at a very precise point. That may not even do it, for he has powers she has never seen before. His blood is toxic and leathal when exposed to humans.
The Gregors are the clones of two visitors from the 1940s, who came to peacefully inherit the Earth from humans do not appreciate it. They are searching for a way to beat their identical natures. Working with fetal tissue, they finally found a way to combine human and alien DNA.
Since the Gregors' project wasn't sanction by their people, the Pilot was sent to eliminate them. Their people consider it a dilution of the species, a pollution of their race.
The Samanthas are just clones of the real Samantha, but they know where she is. The Pilot tells Mulder she is alive.
By lowering the temperature 5 degrees, the alien retrovirus is made dormant and can then be filtered out of the blood safely.
Skinner and X seem to know each other, and Skinner fights X to help Mulder.
Mulder encounters the Pilot and sees him morph and survive a gunshot wound only to infect Mulder. Mulder regains his faith.

Analysis:

How could the Pilot's UFO attack the sub? Either it was running on autopilot, or there was a second Pilot in the UFO piloting it. Considering we see 3 Pilots come out of a UFO in "The Red and the Black", there are likely 2 Pilots sitting in the UFO.
The Navy ordered the sub to shoot the UFO, is this normal standing orders or has the Syndicate informed the Navy that this Pilot is their enemy and to shoot him down? Or is the Navy acting without the Syndicate's knowledge?
The UFO was emitting random radio signals- some kind of alienese communication with the Pilot?
How could the UFO shut down the nuclear reactor? Maybe the systems short out the UFO caused created an automated reactor shutdown, or maybe the UFO (unlikely) able to control the reactor, and insert the cooling rods thus killing the reaction. If this is true, then they would just have easily been able to remove the cooling rods, and create a reactor meltdown. If they can do this, imagine their destructive ability towards nuclear submarines and power plants!
Samantha is able to sense the Pilot's after-presence as well.
When Samantha says she knows how to kill him, she must be extrapolating on to the Pilot the weaknesses of her own species. The Gregors and Samanthas here are killed by the Glimlet to the back of the neck, so Samantha must know that they are weak clones of the Pilots and assume they have the same weaknesses. Then again, since The Pilot has powers she's never seen before, she has never before seen a Pilot (at least use his powers). So it's probably just general knowledge as to their origans.
Samantha says the neck stab must be precise. Mulder stabs The Pilot's neck in "Herrenvolk" and The Pilot survives; maybe Mulder missed, or maybe The Pilot truely is immune to the neck stab. In any case this suggests that the delicate alien organ there is very small; from "Emily" we have hints that the alien nervous system grows there.
From Samantha's (dubious) description of the Gregors, they are two renegade Colonists who came around the Roswell era to form a peaceful slow takeover of the Earth using their clones. Of course, this is about the same time the Colonists first arrived, so more likely Samantha is lying here and the Gregors and Samanthas are just renegade Cloned Hybrids from the Colonist-Syndicate Project. They were working on the Hybrid Program somehow (that's how the Gregors got the alien fetuses).
If the Gregors have found a way to combine human and Colonist DNA, what was the big deal about Cassandra Spender in "Two Fathers" being the first true Human-Colonist Hybrid?
Samantha's story about race dilution and bounty hunters could be a semi-lie as well. These renegade Cloned Hybrids were doing their own experiments risking exposure so the Syndicate called in a Pilot to take them out. Or, the Syndicate didn't know about it, the Colonists did, they didn't like their race being diluted (but isn't that what's going on with the Hybrid Program?) so they sent a Pilot.
The sniper most likely missed the alien organ in The Pilot's neck, so he survived to kill Samantha.
So when a Cloned Hybrid is killed, the alien retrovirus boils away the body. But, if the body is cooled and the retrovirus lays dormant, the body stays. Is this an engineered trait, so that Cloned Hybrid bodies can not be recovered for evidense?
Bill Mulder asks Mulder if it was his decision, the switch. Obviously he suspects Cancer Man's involvement here.
So The Pilot's major objective was to kill this primary Samantha, who was probably a clone of Samantha, and the rest are clones of clones of Samantha and so on. So perhaps one Gregor and one Samantha went renegade, each being clones from the original humans, and then made clones of themselves. Presumably his other big objective was to kill the clone of Gregor, which happened last episode.
I think its safe to assume The Pilot killed the 4 Samanthas including the original, and their bodies boiled away leaving no evidense.
The alien retrovirus is blue here apparantly. Weren't all the alien bacterias in "The Erlenmeyer Flask" green?
X's immeadiate knowledge about this situation reveals the Syndicate's involvement in the situation. It also suggests that the Syndicate is forcing the Navy to search and destroy The Pilot's UFO. Of course, this could all (and most likely is) be a lie to Mulder to concel the Colonist-Syndicate alliance, the biggest secret of the Syndicate.
X also tries to warn Mulder off pursuing The Pilot, saying this is a battle he can't win. Obviously he is trying to keep Mulder away from a Pilot, because he doesn't want his little patsy getting killed or being exposed to the real truth about the aliens, which even X is not prepared to reveal to Mulder (nor was Deep Throat!). X's statements reflect the Deep Throat lie that the Syndicate is out to kill aliens and not work with them.
If X refused to help Mulder, how exactly did he find that submarine when all he knew was that it was in the Artic?!
Skinner appears to know X, or maybe he just knew whoever would enter the elevator would be the man. If he knew X, it would be in associate with Cancer Man most likely.
Why would X help Scully find Mulder? To save his life so Mulder can continue to be a patsy, but what if Mulder learned too much from The Pilot?
So what really happened to the sub's crew? Did The Pilot really kill them all? If they were exposed to the alien retrovirus, they should display irritation around eyes and nose like Mulder did in "The Erlenmeyer Flask". Why would The Pilot kill the crew, when he is so reluctant to kill Mulder? Perhaps he has orders from Cancer Man not to kill Mulder since he is an unknowing Syndicate patsy.
I doubt The Pilot threw Mulder down on the ice so that he would be crushed by the aeroplanes since he saved his life earlier; furthermore by throwing him out on the ice he saves Mulder from the alien retrovirus, and must assume someone will along to rescue him soon.
Why exactly is The Pilot leaving in the sub? If it's to get to his UFO, how does he plan to make the transition? Is the UFO somehow able to dock with the submarine hatch? Can the UFO create a field of air in the ocean for the transfer? Does The Pilot just plan to flood the sub upon leaving then swim to the UFO? This would mean there is some kind of airlock in the UFO or it would be flooded to.
Yet the submarine disapeers; if it were left in the water it would surely have been found. Don't tell me the UFO took it with it?! The UFO was only 80 feet across! Most likely the sub was destroyed into fragments.

FEARFUL SYMMETRY

The Run Down:

A female elephant disapeers out of its locked Idaho zoo cell and reappears 43 miles away, invisable, rampaging down a street. It soon dies of exhaustion. An autopsy reveals it was pregant. Mulder consults the Lone Gunmen; the zoo has a history of animal disapeerances, an animal there has never taken a pregnancy to term, and it is near a UFO hot spot and Airforce Base.
A radicalist breaks into the zoo while the animals go crazy. A tiger disapeers from its cage and reappears outside the cage invisable to maul the radicalist. The tiger is later found visable miles away, and is killed during the captur when it attacks someone. The tiger was also pregnant.
Mulder asserts aliens are abducting and impregnating the animals to harvest their babies, to preserve these species before they go extinct. But there is a problem with returning them, with an astrological variation or trouble with the space-time continuum, and they are returned a few miles away from the zoo.
Also at the zoo is a sign language speaking gorilla Sophie. Recently she has become depressed, wanting a baby. The courts are threatening to return her to Africa. Mulder has Sophie questioned; she is afraid of the light, of her baby going flying with the light. Mulder gets locked in the room with Sophie when she is going crazy; she shortly disapeers in a flash of light. Just before being taken, she signed to Mulder "Man save man".
At the end, Mulder narrates: He thinks it was a judgement upon the increased extinction rate thanks to man. "Our own fate and existance could finally be dependant upon the conservatorship of an extraterrestial race" ie will man save man.

Plot Points:

Some aliens are preserving animal species by impregnating then harvesting abducted animals. These aliens can teleport the animals out of locked environments, but have trouble returning them; they are teleported back miles away, invisable, and crazed. Animals also grow enraged when an abduction is about to happen.
One of the animals left a message: the aliens will save man as well; the fate of humanity is dependant on aliens saving us.

Analysis:

I'm confused; Mulder asserts they are returned 2 miles away, yet the elephant is 43 miles away before anyone notices it. Are we supposed to think that it ran for 41 miles along the road with no one noticning it?
Animals always seemed unnerved by alien appearances; in "Biogenesis" the alien Aritfact fragments drive monkees crazy.
These harvested animals are left barren. So are the harvested female humans that the Syndicate abducts! Is it just a similar connection in technology? These aliens are obviously not the galaxy-conquering Colonists/Purity, they are more likely the peaceful aliens that the Syndicate (and thus the Colonists) are enemies of. So when the Syndicate is after a non-renegade Hybrid alien, it a (let's call 'em Whiteout) alien. So the "Fallen Angel" alien was the same type, the "Little Green Men" alien, and now these. These aliens are peaceful and just want to help the Earth species survive.
When Sophie says "Man save man", thus indicates that to her the aliens and humans are identical, at least to her. Or maybe since she didn't have a word to describe the aliens she calls them man. In any case this definitely NOT the Syndicate at work (they don't have teleportation technology) and is most likely not the Colonists.
Mulder's final note that perhaps the fate of humanity is dependant on aliens is very ironic, since we learn that the Colonists created humanity in "The Beginning" and "Biogenesis".
Perhaps this final statement ultimately means that humanity will be saved from the Colonists by the Whiteout aliens, either by direct military intervention or by abducting a small number to preserve the species.

F. EMASCULATA

The Run Down:

A scientist in the Costa Rican rain forest is infected with a disease and dies. An infected specimen is sent to a similarly named prison convict, who becomes infected. Two prisoners are brought in to clean his room, but escape with the laundry. The National Guard takes control of the prison, Mulder and Scully are called in by Skinner for reasons unknown. All the inmates are infected and dying quickly.
The inmates infect a man, who once discovered by the feds is quickly taken away by men in containment suits on a copter. The feds didn't order it. The inmates hide with a girlfriend. Scully learns the package was sent by one of the largest pharmaceutical (drug manufacturer) companies in the US. The doctors in the prison are not CDC but the company. The disease attacks the immune system and is carried by insect larvae. The doctors are burning all the infected bodies, destroying all the evidense. A sympathic doctor tells Scully that this is an isloated incident.
Mulder visits Skinner and finds Cancer Man there too. He complains that they were mislead about the case. Cancer Man questions what he knows about the disease. Cancer Man says by controlling who knows about a disease, panic and more infection is averted. Mulder says he can't protect the public by lying to them, Cancer Man says its done every day.
Feds find one of the inmates dead, but the other escapes. The escapee is cornered on a bus, and Mulder is about to elicit a statement from him when one of the snipers kills him.
Mulder tells Skinner the outbreak was arranged to circumvent years of FDA testing to put a new drug on the market. He plans to go public, but since it can all be blamed on a postal error it would only discredit him, that's why he was brought on the case. Skinner tells Mulder "You really have no idea of who you're dealing with, do you? I stand on the line that you keep crossing... I'm saying this as a friend. Watch your back. This is just the beginning".

Plot Points:

Cancer Man is associated with major drug companies, who use the National Guard and prison systems to their own illegal ends. This is a continuing thing, and the public is lyed to about it every day.
Skinner tells Mulder he is on the line that Mulder keeps crossing, and warns him this attempt to discredit him was the beginning.

Analysis:

Mulder last saw Cancer Man in "One Breath", where he almost killed him for abducting Scully then leaving her to die. Here he meets him again in Skinner's office, and proceeds to hold a civil conversation with him, answering all his questions! Shouldn't he be acting a bit differently to this man?
So while ultimately the objective was to test a drug without bothering with the FDA, to a lesser extent it was also about trying to discredit Mulder if he goes public with what he knows.
If the objective is to circumvent the FDA, then it's surprising that Cancer Man and the Syndicate haven't been able to infiltrate the FDA when they've obviously infiltrated other more important organizations. Or maybe it was an elaborate scheme to discredit Mulder!
Skinner knows that Cancer Man is planning a big scheme to discredit Mulder, this case just being the beginning. This most likely refers to the doping of Mulder's apartment building water supply, causing him to act irrationally and even punch out Skinner. Viewed from the public eye, here's an FBI Agent who first makes wild baseless accusations about a medical conspiracy then punches out his boss.
Skinner says he stands on the line that Mulder continually crosses, which he does cross slightly sometimes to help Mulder.
Why suddenly set up this big scheme to discredit Mulder? The best reason is Mulder's recent exposure to true aliens; Hybrids and Pilots and alien retroviruses in "Colony" and "End Game". By now having seen true aliens, he is a much larger threat.

SOFT LIGHT

The Run Down:

A scientist, Banton, goes to a hotel to meet his collegue Morris. Watching him in the opposite room is a Morley tobacco employee, and when Banton's shadow falls across the employee, he is sucked into it. There have been other missing persons, with the strange scorch marks. Banton worked for Polarity Magnetics to research dark matter, and was involved in an accident with a particle accelerator that burned his shadow into the wall. His colleague Davey was a witness to accident, and tells Mulder and Scully so.
Banton runs into a police patrol, and they are killed by his shadow. Mulder and Scully find him and capture him (by Mulder shooting out the nearby lights). Banton tells them his shadow has become a black hole, converting matter into energy. He says he is being sought by the government, who can't wait to their "brain suck" on him and steal his knowledge.
Mulder contacts X and they meet. Mulder tells him about Banton. X says he can't help, "the last time I helped you I bloodied my fist and regrettably exposed my identity to associates of yours". Mulder says he can trust them. X says "dead men can't keep promises. The next time the blood and regret could be yours. I'm not at your beck and call... I have nothing to gain and everything to loose by helping you. Promise you won't contact me again unless absolutely necessary". X leaves.
At Banton's cell there is a power outage, and X shows up with two men to 'transfer' Banton. The emergency lighting comes on and Banton's shadow kills the two men. X pulls a gun on Banton, keeping away from his shadow. Banton flees. Scully later finds the power was taken out by a government imposter who knew what he was doing.
Banton goes to Polarity Magnetics, and gets Davey to help him activate the partical accelerator to deactivate his shadow. Once Banton is locked inside the chamber, Davey reveals he is working with the government, and calls them to say he has Banton captive. Davey is shot... and X appears looking in on Banton. Mulder and Scully arrive to see the accelerator activate, destroying a body inside the cell. Mulder later realizes the body destroyed was Davey's when Davey goes missing.
Mulder meets X again, and says he knows X used him to get Banton. Mulder says "I won't be your stalking horse, or the government's". X says "you seem to be mistaken on the amount of control you exercise over this arrangement". Mulder asserts he's killed Banton and asks who he answers to. X says "despite my loyalty to my predecessor, I've never made you any promises". Mulder says their relationship is over. X says "you're choosing a dangerous time to go it alone" and says he didn't kill Banton.
X visits a scientist at a government hospital. The scientist says Davey would have been helpful to us, "we'll be studying this man for a long time". Banton is in a cell attached to sensors, a flashing light is casting his shadow on a photoelectric panel.

Plot Points:

The government has the ability of the "brain suck", which apparantly steals a person's memories.
X is angry at Mulder for having been exposed to Skinner and Scully, and warns him to only contact him on vital cases.
A scientist absorbs dark matter, and his shadow is a mini-black hole. X has this man captured for study by the government.
Mulder wants to break off with X, but X warns him its a dangerous time to go alone.

Analysis:

Was it really a coincidense that the man in a hotel room across from Banton's buddy is a Morley tabacco employee? It seems likely that Cancer Man had this man put there to watch for Banton. It's an interesting connection that Cancer Man has actually infiltrated the company that makes the cigarettes he smokes!
I'm not going to dwell on a scientific matter, but I wonder why only people were sucked in to the shadow. Why not walls it fell across? If the rule is organic matter only (and why would it differentiate?), then the clothes (non-organic items) on the sucked people should remain.
The "brain suck" may be what Mulder was subjected to in "Deep Throat" when they erased his memories of his UFO encounter. Furthermore, it could be an offshoot of the lost time effect of UFO close encounters.
If X was interested in Banton, it must have only become from what Mulder told him at their first meeting. Because Mulder and Scully were brought onto the case as a personal favor to Scully's protoge.
X shows up very quickly after Davey calls, so perhaps X was following them and Davey didn't call X.
X shoots Davey and the government scientist later says they could have used Davey. Why did X kill him then? Was it against the Syndicate's wishes, and by killing Davey he knew the Syndicate would never really learn anything from Banton, a sign that he really is working against the Syndicate? There seems little other reason to kill a fellow conspirator.
Mulder asks who X answers to, but X never answers him. The answer, of course, is Cancer Man!
X warns Mulder he's choosing a dangerous time to go it alone. This ties in to Skinner's warning to Mulder in "F. Emasculata" that it was only the beginning of attempts to discredit him. This suggests that X is aware of the doping of Mulder's apartment building water supply, hell he's probably in charge of it.
Mulder breaks off with X here. When he tries to signal X regarding the DoD files in "Anasazi", X does not answer. In fact, X doesn't appear again until "Nisei" next season, and then it is only to Scully though he saves Mulder's life. After that, he doesn't appear again until the end of the season in "Wetwired" (and "Talitha Cumi"). So this episode actually marked a major seperation between Mulder and X, and the end of their regular informant relationship!

ANASAZI (part 1 of 3)

The Run Down:

An earthquake shakes New Mexico. A Navajo, Albert Hosteen, says "the earth has a secret it needs to tell". His grandson Eric rides out to a canyon, where he finds the top of a large metal object buried in the sand. He brings back something and shows it to the townsfolk; Albert says "it should be returned. they will be coming". It is the mummified corpse of a short Hybrid alien.
Lone Gunmen ally The Thinker hacks into the DoD computer system. He manages to copy some files to a DAT tape. This sparks an alarm in the United Nations Italian office, who say "someone has broken into the MJ documents". They call the Japanese, who say "from where did you hear this? has everyone been told?". They call the Germans, who says "no this is their problem. they must take care of it promptly". He calls Cancer Man and says "you are familar with the MJ file?". Cancer Man assures him it's already taken care of. Cancer Man is in a darkened office with several men; he tells them "that was the phone call I never wanted to get". BlackOps troops break into The Thinker's apartment and ransack it, but he is not there.
The Lone Gunmen visit Mulder at his apartment; he has had trouble sleeping with a fever and is irritable. They are being followed by Garnett- a multinational black ops unit, trained killers, School of the America Alumni. Garnett is after Kenneth Suna- The Thinker. He contacted them in order to meet Mulder. In Mulder's building, a woman irrationally kills her husband. Mulder meets The Thinker, who claims to have "the original defense department's UFO intelligence files. everything from the 1940s and up... Roswell, MJ12 and beyond". He didn't read them all, just downloaded and ran since he didn't use security cautions (he didn't expect to break in). He gives Mulder the DAT tape in return for the promise that the truth is revealed and these bastards answer to the people.
Mulder opens the files (DoD Top Secret) in his office with Scully; it appears to be gibberish but Scully recognizes it as Navajo code which was used in WWII since it was the only code the Japanese couldn't break. Scully goes to find a translator. Skinner meets Mulder, and accuses him of receiving sensitive files. Mulder gets enraged and decks Skinner. Scully is called to testify to the OPR Board about Mulder's behavior. They threaten Mulder with being fired and Scully with the same if she witholds information.
Cancer Man visits Bill Mulder at his home. Bill is shocked, and says "we agreed that you would never-". Cancer Man says "that was a long time ago, Bill. there have been some unforseen events". Bill "no one was supposed to know". Cancer Man "who could have predicted the future, Bill? that the computers you and I only dreamed of would someday be home appliances capable of the most technical espionage". Bill "the files should have been destroyed". Cancer Man "they should have but they weren't. regret is an inevitable consequence of life". Bill asks how he knows its Fox, Cancer Man says "the man who stole them has come forward. as always we maintain plausible deniability. the files are only as real as their possible authentication". Bill "my name is on those files". Cancer Man "the files have been encrypted of course. we have a luxury of time. we endevored to prevent that fact from ever coming to light". Bill "you wouldn't... harm him?". Cancer Man "I've protected him this long, haven't I? Your son has been provident in the alliances that he's created. the last thing we need is a martyr in a crusade". Bill "but if he should learn of my involvement...". Cancer Man "you're your own man, Bill. you always have been. but I strongly encourage you in that event, to deny everything. it's been good to see you again, Bill. you look well". Cancer Man leaves.
Mulder sets the signal for X. Scully meets a Navajo translator with some MJ file printouts. She can only recognize a few words, but will set Scully up with a real code talker. there are some modern words which are recognizable; goods/merchandise and vaccination. Bill calls Mulder to his house. Scully arrives at Mulder's apartment, and when she approaches the X signal on the window she is shot at. A car drives off.
Mulder meets Bill. Bill says "it's so clear now. simple. it was so complicated then. the choices that needed to be made... you're a smarter man than I ever was. your politices are yours, you've never thrown in. the minute you do that, their doctrines become yours and you can be held responsible. you're going to learn of things, Fox... you're going to hear the words, and they'll come to make sense to you. the merchandise". Bill goes to the bathroom to take some medication; Krychek is waiting inside. A gunshot rings out, and Krychek is gone. A car drives off. Bill dies in Mulder's arms, saying "forgive me".
A distracted Mulder calls Scully to tell her, she has him come to her apartment. Scully takes Mulder's gun and the DAT tape. She has the gun tested to prove it wasn't used to shoot his father. Mulder becomes enraged and leaves. Scully digs the bullet out of Mulder's wall and sees an unmarked truck. She finds a filter on the apartment's water supply. Mulder finds Krychek sneaking around outside his building, and jumps him. He accuses Krychek of killing his father, and is about to shoot him (with Krychek's gun) when Scully puts a gun on Mulder. Mulder is loosing control and is about to kill Krychek; Scully shoots him and Krychek runs away.
Mulder wakes up in New Mexico with Scully and Albert. She shot him because if Mulder killed Krychek with the gun that killed his father, he would have been framed. The water filter was doping Mulder's apartment water supply with something, most likely LSD. Albert has been translating the MJ file; he was a Navajo code talker during WWII, "he helped encode the original government documents". Albert says he knew Mulder was coming; "last week we had an omen". From the files; "there was an international conspiracy of silence dating back to the 1940s". Albert says evidense of these secrets are buried not far from here. He'll take Mulder there. Since Scully didn't show up for a meeting with OPR, she's probably out of a job. Scully's name is in the MJ file, "in the latest entries with Duane Barry... it has something to do with a test".
Mulder asks Albert how he knew he was coming. Albert says "in the desert, things find a way to survive. secrets are like this to. they push their way up through the sands of deception so that men can know them". Mulder is the one because is "prepared to accept the truth, to sacrifice [himself] to it... there was a tribe of Indians who lived here more than 600 years ago. their name was Anasazi, it means ancient aliens. no evidense of their fate exists. historians say they disapeered without a trace. they say that because they will not sacrifice themselves to the truth; nothing disapeers without a trace. [they were abducted] by visitors who come here still". He says "lies" are buried out there. Albert's grandson Eric takes Mulder to the canyon.
Cancer Man calls Mulder, saying he needs to talk to him in person, some things need explaining. Cancer Man says "your father may have told you things, I should warn you against taking those things at face value. he was never an opponent of the Project. in fact he authorized it. that's what he couldn't live with. we weren't involved with that [Bill's murder]". Mulder threatens to expose the Project, Cancer Man says "expose anything and you only expose your father". Mulder hangs up, but Cancer Man was able to trace Mulder's location. He takes off in a helicopter with a team of Army soldiers.
Mulder inspects the metal object; it is a Sierra Pacific Railroad refrigeration boxcar. Inside are stacks of Hybrid bodies. He calls Scully; in the MJ file are references to "experiments that were conducted here in the US by Axis power scientists who were given amnesty after the war. some kind of tests, on humans. what they referred to as merchandise". Mulder finds smallpox enoculation scars on the arms of all the Hybrid bodies.
Eric closes the boxcar hatch, leaving Mulder trapped inside as a helicopter approaches. The troops search the area and the boxcar but can't find Mulder; "he's vanished without a trace". Cancer Man says "nothing vanishes without a trace! Burn it!". The troops torch the boxcar and the helicopter leaves...

Plot Points:

An earthquake exposes a boxcar full of Hybrid bodies bearing smallpox enoculation scars. At the same time, The Thinker hacks into DoD and downloads the MJ files into a DAT tape.
The MJ theft alarms the Italians, Japanese, and Germans who demand Cancer Man solve the problem. The Thinker gives the DAT tape to Mulder shortly before being captured by Cancer Man.
Garnett is a multinational black ops team, trained killers from the School of the Americas. They do Cancer Man's leg work here.
Mulder has been acting irritable lately; it is because of the doping of his building's water supply which causes him to punch out Skinner, getting him threatened with being fired from the FBI, along with Scully for not giving information and missing a meeting.
Enter the MJ files; the DoD's complete knowledge of UFO intelligence since the 1940s including MJ12 and Roswell. Bill Mulder's name is in the files. Scully's name appears in the latest entries with Duane Barry's referring to a test. It involves merchandise and innoculations. It details an international conspiracy of silence since the 1940s, and experiments conducted in the US by Axis power scientists given immunity who tested on humans-merchandise. the files are encoded in Navajo code; it was the only code the Japanese couldn't break in WWII.
Bill Mulder and Cancer Man used to be close friends, but they agreed to stay apart now. Cancer Man warns Bill to deny the truth to Fox should it come out.
Cancer Man has been protecting Mulder all this time with the martyr to the cause excuse.
Bill begins to tell Mulder the truth; he allowed others to decide his doctrines, and he became responsible for it. Krychek kills Bill before he can tell anymore.
Mulder finds Krychek outside his apartment and almost kills him; Scully shoots him and lets Krychek escape.
Enter Albert Hosteen: a Navajo who was a WWII code talker. He is a believer in aliens and helps Mulder decode the MJ files.
Scully takes the DAT tape from Mulder.
Mulder is trapped inside the boxcar when Cancer Man arrives by troops. When the troops can't find Mulder Cancer Man orders the boxcar burned and leaves.

Analysis:

Albert seems to possess some elemental knowledge of the earth; he senses that the earth has a secret to tell. He is also a firm believer in aliens and says they come here still; has he been abducted by aliens, and is he in some form a Hybrid which gives him extrasensory abilities (like Cassandra Spender in "Two Fathers")?
I'm confused how an earthquake unearths a boxcar buried in a flat plane of sand, since there was no sign of an open fault in the area. It would seem that a ton of sand was somehow displaced from above the buried boxcar; how?
It it just a big fat raging coincidense that the earthquake happens at the same time The Thinker accidently acheives the impossible and breaks into the DoD computer systems? I'd rather think that after the earthquake, someone accessed the DoD files to check up on the the danger of anything being exposed by the earthquake, which somehow caused a security fault which allowed an 'unprotected' Thinker to access the files.
Albert said it should be returned, they will be becoming. This suggests that he knew that the boxcar was sitting there under the earth filled with evidense of the Project. Why the hell didn't he tell anybody? In subsequent episodes Albert is quite willing to help believers, so why has he kept the secret? Maybe he was waiting for the one who was willing to sacrifice him to the truth, as Mulder was. That actually makes sense given the mythical nature of Albert.
Who does Albert think will be coming now? Presumably the Syndicate men. Yet he says this refers to Mulder to Mulder; so when the truth was unearthed he knew it meant the one who would sacrifice himself to the truth would be coming. If so, why did he want it returned? So the one/Mulder would have to see it himself? Probably.
I assume Eric and the others did return the Hybrid corpse to the boxcar. For that matter, how did Eric transport this corpse home? Did he have it riding shotgun on his motorbike with him?!
Notice the three foreign nations alerted to the MJ theft (Italy, Japan, Germany) were the three Axis powers in WWII! The immeadite implication is that the Syndicate is allied with these three nations now (or was previously). The fact that Axis scientists came over to the US does not really involve those nations' governments. However, later episodes ("Nisei" and "731") shows that there is a secret war going on between the Syndicate and Japan, so this suggests that these people are only alerted because of their indirect involvement through the defecting scientists. They are not part of the Project, but they will be implicated by it.
This is supported by the German saying no this is their [the Syndicate's] problem. Also, the German asks if Cancer Man is familiar with the MJ documents. He could have been speaking in a questioning mannor, but maybe since he's not connected with the Syndicate he truely doesn't know if Cancer Man (who he would barely know) knows about the MJ documents.
Also notice that the three people were alerted in their positions of strength in the war; Italy, Japan, Germany.
Cancer Man is in a room with several men. Since he's a desk and they aren't, it's safe to assume these are Cancer Man's assassins (aka his bitches) and not the Syndicate Elders (otherwise they'd be the ones at the desk).
So the troops dressed in black are Garnett, the premiere BlackOps troops, though occaisionally US military troops are used like Cancer Man at the end of this episode.
The MJ documents are in the only code the Japanese can't break- another indication that the Syndicate are enemies of Japan.
The OPR Board is not neccessarily in with the Syndicate/Cancer Man. They could just as easily be unwittingly doing the Syndicate's work in trying to discredit Mulder.
If Cancer Man (and Bill Mulder) wanted the MJ documents destroyed, why weren't they? Did Well-Manicured Man and the Syndicate Elders intercede?
Cancer Man made an agreement with Bill Mulder to stay away from him, presumably after Samantha's abduction and the Colonist-Syndicate alliance in 1973.
This episode alledges that Cancer Man protects Mulder as a favor to Bill, but the truth is more personal; Cancer Man sees Mulder as a pseudo-son so protects him.
Cancer Man says Mulder has been provident in the alliance he's created. So this means the martyr excuse only works because Mulder keeps friendly with his friends in the Senate (and perhaps with X, a Cancer Man spy on Mulder?).
Cancer Man mentions that Bill has always been his own man. This may true since 1973, but before that as Bill admitted to Mulder he allowed others to dictate his actions. This all means that the Group/proto-Syndicate was formed after Roswell in 1947 in the US State Department (though Cancer Man claims to Mulder that Bill created it he was probably lying to keep Mulder from exposing the truth by saying it would only expose his father), and Bill wasn't happy about it but he allowed others like Cancer Man to make his decision for him. But in 1973 when the Syndicate decided to ally with the Colonists and let them take their children, he decided to make his own decisions.
Who shot at Scully? Maybe it was X, trying to kill Mulder for daring to involve him in such a dangerous case. Maybe it was Krychek, trying to kill Mulder as he was ordered. Maybe it was Krychek, because through Cancer Man he knew the taped 'x' means Mulder is waited for X to call him, which means X is a Cancer Man spy on Mulder. Or a generic Syndicate assassin for the same reasons. But Krychek later appears outside Mulder's building waiting to ?kill? him, so he's likely. BUT, Cancer Man shouldn't be trying to kill Mulder (unless the importance of the DAT tape superceedes his concern for Mulder).
Bill told Mulder the words would come to make sense to him. Does this mean that Mulder will come to understand why they committed these atrocities (to save humanity from alien invasion), or simply the meaning of the words? Since Bill's hope was that Mulder would "fight the future" (see The Movie), maybe the first.
Krychek did not neccessarily kill Bill, though it's certainly likely. Someone may have been with him, as Luis Cardinal accompanied him to the Scully hit in "The Blessing Way". Surely he was sent by Cancer Man to kill Bill if he started to talk to Mulder (if Cancer Man is willing to kill his old friend Bill I suppose its plausible that he's willing to kill Mulder as well).
What exactly was Krychek doing outside Mulder's building? Was he going to enter to try and kill Mulder, or just see if he's there. Here's a better option; he was going to search Mulder's apartment for the DAT tape. Maybe Krychek was sent by Cancer Man to be killed, thus framing Mulder for the murder of his father as well!
Scully says Albert helped encode the original government documents. I sincerely hope that this refers to the WWII stuff, and not the MJ documents! Then again, Albert was aware of the Hybrid bodies in a boxcar under the sand! If he did code the MJ documents, then he should REALLY be telling Mulder the stuff he learned.
The MJ files refer to an international conspiracy of silence since the 1940s; this sounds like the meeting Deep Throat referred to in "E.B.E." where all the nations in the middle of the Cold War agreed to kill any aliens. If this agreement is true, then the Americans/Syndicate is REALLY breaking this law.
Scully, Duane Barry, and a test are in the latest entries. Maybe the updating of the files recently is what caused the security lapse that allowed the Thinker to hack them.
Notice Scully uses the plural "entries" concerning her in the MJ documents. It's interesting that Scully gets several entires, when she was only abducted for a month. Just how damn big are these files if Scully gets this much space?!
The test is of course the Hybrid birth program, or maybe a Black Oil Vaccine testing program. Barry being in the same place suggests that Barry was abducted to be experimented on just like Scully. Of course he couldn't have been given a Hybrid baby, but Mulder says in "Field Trip" that male abductees do sometimes get Implants, so maybe he was given the Black Oil Vaccine test. Then again, "Terma" shows the Syndicate uses elderly homes for this, but "The Pilot" suggests abductees being tested with Black Oil.
Albert knows that the aliens continue to visit Earth.
Why did the Colonists abduct the Anasazi? Perhaps it was the nice Whiteout aliens from "Fearful Symmetry" who wanted to preserve a soon to be extinct species.
Cancer Man was definitely lying to Mulder, trying to convince him not to expose the MJ documents. Also, he didn't know how much Bill told Fox so he had to assume that Mulder now knows a substantial bit about the Syndicate and the Project.
The truth about the Hybrid bodies: before the Colonist alliance of 1973, the Syndicate tried to create an alien-human Hybrid themselves (which would somehow give them a Vaccine against the Black Oil), as seen in missing scenes from "One Son". These bodies are the evidense of one of these experiments; innocent Americans were experimented on to make Hybrids (somehow involving smallpox ennoculations which probably had more to do with cataloging than biological changes) but these things failed. So the failed experiments (which were experimented on in roving boxcars as seen learned in "731") were killed then buried in boxcars in the New Mexico desert. Also, in the "One Son" missing scene a Native American was being experimented on. There is a big connection here between pre-73 Hybrid experiments and the Native Americans. Plus, First Elder seems Navajo and he was apparantly in charge of the Hybrid train stuff in "731"!
Cancer Man is very distressed to hear the phrase "disapeered without a trace". Does he have a history with Albert, or has someone like Albert (another Navajo? First Elder, Cancer Man's rival?) said this phrase to him?

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