X-Files Mythology Guide Season One

Mythology Guide: Season One

THE PILOT

The Run Down:

Agt Scully is assigned to Agt Muldar to debunk the X-Files division by Section Chief Blevins. Alongside him is FBI Senior Agent and Cancer Man. Muldar initially distrusts her as a spy but comes to trust her.
The Oregon abductions leave victims with scars on the back which carries an organic (possibly synthetic protein) substance. This also appears in South Dakota and Texas. The abductees are drawn to the forest where one abductee supervises their abduction; they are found dead the next morning. The abduction: bright light and loud noise, wind blasting. One victim has schizophrenia, one is comatose, one suffers rage fits and has nose bleeds. They all have the scars on the backs.
Over Oregon the plane has a temporary power failure. At a spot on the road the car radio goes crazy, and later causes a white flash and a missing nine minutes for Mulder and Scully.
The decayed bodies of the victims resemble Little Greys. The bodies are mammalian, 156cm long, weigh 52 pounds, have large eye cavities and a large skull. There is an unidentifyable metal implant in the nose.
At the forest spot, the compass goes crazy and there is some kind of sand there.
Mulder's sister Samantha (age 8) was abducted when he was 12. She disapeered from her bed, there was no evidense and it tore the family apart. With regressed hypnosis Mulder can recall seeing a bright light outside and a presence in the room, being paralyzed while his sister called for help.
Mulder has recently found the X-Files but is being denyed access to classifed government information by someone. The only he reason he's still around is because of his friends in Congress. Mulder knows why she was sent.
The rage fit abductee was killed by a truck while running to the forest. She was missing the same nine minutes that occured to Mulder and Scully. While they were gone, the autopsy lab was ransacked, the body stolen, the remaning graves of dead abductees stolen, and the hotel where Scully's evidense was was burned. The last abductee comes to them, who also suffers nose bleeds.
Mulder asserts the comatose boy is killing the abductees, that something in the forest controls them and summons them; the marks are signs of some test of genetic mutation. The comatose boy did take the rage fit abductee where she was killed by the truck. They track the comatose boy, who under control is presenting the last abductee as the light approaches. The abduction occurs, the girl disapeers, the boy is now normal without test marks.
Under regressed hypnosis the boy remembers the first night, being taken to "the testing place". He was assigned to gather the others for the tests, they put in a nasal implant. He would wait for their orders, "they" said no one would know. But the test didn't work so they wanted everything destroyed, said they were leaving.
Blevins is skeptical of the case until Scully produces the only remaining evidense; a nasal implant. She gives it to Blevins, she then sees Cancer Man entering Blevins' office. Cancer Man later deposits the nasal implant in a large chamber filled with similar evidense boxes. This box has 7 holes and is now filled by 6. The chamber is deep in the Pentagon, where Cancer Man has a security card to access it.

Plot Points:

Scully is assigned to debunk the X-Files by FBI Section Chief Blevins and FBI Senior Agent.
Enter Cancer Man: a silent man smoking cigarettes who oversees the DC side of the abduction coverup. He can make Blevins and Senior Agent do what he wants and has access to the Pentagon Security Vault. Cancer Man is out to debunk the X-Files.
Someone is responsible for covering up the evidense of abductions, represented by Cancer Man.
Abducted bodies have been discovered in Oregan, North Dakota, and Texas with marks and the protein.
Abductees have marks on their backs which carries an organic substance, possibly a synthetic protein. They also have unidentifyable nasal implants. They can be controlled by the abductors and be drawn to the place of abduction.
The abductors are killing these abductees because their test (involving genetic mutation) did not work.
The unseen UFOs have the following side-effects/abilities: causes power failures and disruptions in electronic equipment, causes disruptions in the magnetic field, sand, bright lights, loud sounds, wind gusts, and missing time (9 minutes).
The abductee bodies resemble Little Greys. Large eye cavities, flattened skull, 156cm long, weight 52 pounds.
Mulder's sister Samantha was abducted when they were children; there were bright lights outside, a presence in the room, and Mulder was paralyzed.
Mulder is being denyed classifyed government information.
Mulder is only able to stay on the X-Files because of friends in Congress.
When Scully hands over to Blevins the only remaining evidense (a nasal implant), Cancer Man soon receives it.
The Pentagon Security Vault holds the secrets of the government, including evidense of abductions.

Analysis:

Cancer Man has high influence in the FBI, all the way to the top of the command structure. He wants to debunk the X-Files, thus discrediting Mulder's discoveries so the truth of abductions is never discovered by the public. He seems to operate solely out of DC here, mainly a contact to the FBI on behalf of the Syndicate.
The Syndicate and/or BlackOps/NSA are responsible for the abduction coverups.
These marks on the back resemble smallpox scars (which appear later in the series) which carry identification tags, the way these marks carry an organic compound. Was this a proto-type of that concept, as it never appears anywhere else?
It is likely that the Syndicate are the abductors, and that they were exposing their abductees to the Black Oil. Given future episodes, it is shown that alien abductions are rare that it is usually the Syndicate at work. The marks carry an organic compound (Black Oil is organic), which might be a synthetic protein (Black Oil is a synthetic protein!). If it is so, this explains why the corpses resemble Little Greys. Black Oil (when used at 90 degree plus temperatures) causes the host to gestate a Gestated Grey, which then transforms into a Little Grey ("The Beginning"). This would then be an early case of the Syndicate looking for a Vaccine to the Black Oil by exposing humans to it while trying to give them something that would kill the infection.
Considering the condition of the abductees afterwards, they are either being exposed to minute amounts of Black Oil or the Black Oil is somehow being filtered out of their blood after the tests. Or perhaps it is dead or weakened Black Oil (the essential concept of a Vaccine is to send the dead/dying virus into the blood so the immune system can defeat it, and it will then know how to fight the virus normally).
The nasal implants resemble the neck implants that appear later in the series; presumably another concept proto-type.
The nasal implants are what is being used to control the abductees and draw them back to the abduction place. This concept is seen later in the series ("Duane Barry", "Patient X").
Why kill the abductees? After their exposure (which was not cured but partially removed) they are solid evidense of the Black Oil, the greatest secret the Syndicate has to keep
The Syndicate (through the US Air Force) owns and operates alien-tech UFOs are later shown to be capable of missing time ("Dreamland I & II"), bright lights and loud sounds, magnetic disturbances ("EBE", "Little Green Men"), but never sand or curious wind gusts again.
Was Mulder (during Samantha's abduction) somehow paralyzed by the abductors?
Mulder is surprised he is being denyed classifyed government information. Why? Isn't it classifyed? Why does he think he should get access to information about his security level?!
We later see one of Mulder's friends in Congress: Senator Matheson ("Little Green Men").
Cancer Man and the Syndicate is in the business of hoarding abduction evidense in a Pentagon vault, obviously suggesting military complicity. The Pentagon is the headquarters of the Department of Defense (DoD).
There were 7 slots in the implant box, only 6 were filled. Where is the 7th?
Wasn't Mulder suspicious when the nasal implant disapeers when Scully gives it to Blevins? Wouldn't he suspect Blevins as being part of the conspiracy? Is this how he knows to accuse Blevins of being so in "Redux II"?

DEEP THROAT

The Run Down:

At Ellens Air Force Base in Idaho, MPs apprehend Col Buddahas who stole a military vehicle "that's believed to be armed". Buddahas is dazed, shivering, and covered in radiation blisters. He was a test pilot, and has been gone for 4 months. His wife called in the FBI. Since 1963, 6 pilots have disapeering while testing experimental aircraft.
Mulder takes the case but is warned off it by a mysterious man, Deep Throat. He says the military will not tolerate an FBI investigation. He offers his help, says he has an interest in his work, that he is in a position to know a lot of things about the government. He says Mulder has much work to do, this is an uneccesary danger. He runs off.
Mulder's apartment phone is being tapped when Scully calls him about the case.
Mrs Buddahas tells them Buddahas has been having the blisters for 2 years, and his personality has been degrading. He suffers mood shifts and seizures. Other pilots have had nervous breakdowns but have been returned. Mulder asserts it is the Aurora Project (experimental spy planes that fly at suborbital altitudes) which is tested in the Western US. The military is refusing to talk to them but a reporter Mossinger inquires on their progress.
Mulder visits a UFO bar where the barkeeper took a picture of a triangular UFO that hovered in the sky for awhile one day. Ellens AFB isn't on government maps, but Mulder gets directions to it. At the border Mulder sees two lights that dance in the sky at impossible speeds and turns. After a half hour of manuvering they flit into the sky and disapeer. A helicopter then chases out Mulder and Scully along with two teens who snuck onto the base. They've been visiting for a year and were never discovered. One time they dropped bombs. They are observed talking later by Mossinger.
Mulder asserts Ellens AFB is one of the six bases to receive wreakage from the '47 Roswell triangular UFO crash. He thinks the military is flying planes built with UFO technology.
Buddahas is returned, but he is not normal. He cannot remember anything regarding flying. Mulder asserts Buddahas underwent a selective brain drain after becoming a security risk, Scully says it is impossible. Mulder asserts such men are incapable of dealing with the stress of the manuvering the UFOs are capable of. In the name of "national security" black suited men pull Mulder and Scully off the road and confiscate all their evidense, and warn them to leave immeadiately. Their car plates are unregistered. Mulder asserts that the helicopter was chasing off them not the kids, that they knew he was coming all along. Buddahas was returned as a decoy.
Mulder sneaks into the base and waits until night. By an airstrip he sees a triangular UFO which hovers over him and bathes him in light. MPs then storm the area and capture him. He is injected with something. He is carted past the UFO covered with plastic drapes and a doctor attends to Mulder.
Mossinger checks on Scully who hears his military radio. She holds him at gunpoint, his ID card reads Airbase Security. She takes him to the base gate and demands an exchange for Mulder. Mulder is produced, but can't remember how he got here.
Mrs Buddahas has been silenced. The case is closed.
Deep Throat meets Mulder. Deep Throat says he's seen things that were not to be seen. He will provide information only when it is in his best interests; the truth. He confirms Mulder saw a military UFO, and says there is no conclusive evidence against alien life. Mulder says "They're here, aren't they?". Deep Throat says "They've been here for a long long time".

Plot Points:

Airforce test pilots have been suffering from UFO flying since 1963.
Symptoms of repeated UFO flying: erratic mood shifts, nervous breakdowns, seizures, radiation blisters, shivering.
Enter Deep Throat: a mysterious man who warns Mulder off investigating the military UFO pilots. He has offered to aid Mulder when it is in the interests of the truth,
Deep Throat is in the position to know a lot about the government. He knows the military is operating UFOs. He knows aliens have been on Earth for a long time.
Mulder's apartment phone is under surveillance.
Enter the Aurora Project: experimental suborbital spy planes that the US military test flys in the western US and was used repeatedly to obverse Soviet Russia.
The military owns and operates at least two triangular UFOs.
Military UFO capabilites: impossible manuvering, hovering, impossible speeds, emits radiation in some form.
The Airforce test pilots for military UFOs regularly suffer nervous breakdowns, disapeer for several months and then reappear without any memory of flying experiences and slightly retarded.
Ellens AFB is one of six bases to receive wreakage from the Roswell crash in 1947.
The military possess the ability to do a selective 'brain suck' on someone, erasing their memories of something. It involves the injection of a serum.
Ellens AFB security knew Mulder was coming before he arrived, and watched him the whole time. They chased him off when he observed UFOs manuevering and confiscated all his evidense. They later return him to Scully in return for one of their personnal she was holding hostage.
Mulder witnessed up close one of the military UFOs which saw him, but his memory of the event was erased.
According to Deep Throat, Mulder was not supposed to see the military UFO. He confirms it was a military UFO.
According to Deep Throat, aliens have been on Earth "for a long, long time".

Analysis:

If UFO wreakage from Roswell was sent out to the bases in 1947 and the pilots began to suffer in 1963 (the year JFK was assassinated!), perhaps that means it took 16 years to reverse engineer the UFO technology. But considering how closely the Syndicate works with the Colonists, it seems curious that they could keep this project secret from them, or that the Colonists would not just give them the technology. Since the Syndicate is essentially acting as the errand boys of the Colonists (using these UFOs to abduct women and birth Hybrids) it seems highly unlikely that they are using these UFOs without the Colonists knowledge. So perhaps the abduction/Hybrid program did not begin until 1963, or maybe it began before and it just took a few years for symptoms to start.
The side-effects of repeated UFO seem to be brain damage and radiation damage. The brain damage is most likely from the brain being knocked against the skull during a tight turn or stop, in addition to radiation damage.
Why do UFOs leak radiation? Is it part of their drive system?
The unseen UFOs in "The Pilot" did not seem to cause radiation. The missing time in that episode was never substantiated. It thus seems more likely that in "The Pilot" the Syndicate was merely using their stealth copters and sonic weapons to abduct the teenagers and just turned back their watches while they were stunned. Then again, missing time is shown to be an adverse side effect of UFOs in "Dreamland I & II".
Deep Throat appears to have little influence over the military here. Yet later he and the Syndicate can order them around. He was probably misleading Mulder to this truth.
This is the first time Mulder is shown under surveillance; by Cancer Man. We later see that Cancer Man always has Mulder under surveillance in "EBE" and many others; he even probably observed his first meeting with Scully as shown in the theoretical "Musings of Cancer Man".
The Aurora spy planes are of course the military UFOs. They have never been shown to be armed, merely recon crafts that are used to abduct people. The teens in this ep claim to have seen them dropping bombs one time, something which was never substantiated and is likely untrue.
Though only 2 are shown, the military most likely has a whole fleet of UFOs in Western USA.
The capabilites of the UFO all suggest anti-gravity; with no inertia the UFO could move very fast and turn fast and stop fast easily (of course it wreaks hell on the human pilots inside!).
The military's selective brain suck ability most likely has nothing to do with alien technology. It is what allows them to abduct women, use them to birth Hybrids, then totally erase their memories of it. Of course, the memories of the abducted birth women always come back after a year or so.
Was Mulder really not supposed to see a military UFO? Since Mulder plays an important role in the Colonization "equation", making the believers seem ridiculous, wouldn't him believing he saw a UFO help his determination to be the unwitting pawn of the Syndicate?
Deep Throat knows that aliens have been here a long, long time. This doesn't refer to 1947. We learn in the Movie that aliens first visited Earth at least 37,000 years ago but actually millions of years ago! But the fact that Deep Throat knows this puts him at the same information access level as Well-Manicured Man (who reveals this to Mulder). This supports the general theory that Deep Throat was just as if not more important to the Syndicate as Cancer Man.
Buddahas stole a military vehicle believed to be armed. Did this refer to the UFO he was flying and the MP didn't know what it was? Unlikely; he probably just stole a jeep.
Base security was probably just about to let Mulder go anyway when Scully took Mossinger hostage. They obviously couldn't disapeer an FBI Agent for 4 months the way they can their own pilots.

CONDUIT

The Run Down:

Darlene Morris' daughter Ruby is abducted while camping on Okobogee Lake. There was a bright light and extreme heat/radiation (enough to turn sand into glass). Okobogee is a UFO hotspot with 4 sightings in '67 including one by Darlene Morris as a child. The little brother Kevin has since then acted strangely; he has nightmares and watches TV static and writes down binary code.
Mulder requests the file and Blevins shows Scully the X-File he opened on his sister. Blevins insinuates Mulder wants the case because it is similar to his sister's disapperance, Scully tells Blevins Mulder's account of what happened.
Mulder sends some of Kevin's code the FBI and soon NSA agents confront them and demand where he got the information. It's a fragment of a highly classifyed defense satellite transmission. NSA raids the Morris home and grabs the rest of Kevin's code which is binary translations from the Voyager space probe showing humanity's best acheivments; music, DNA, art, etc. Mulder asserts Kevin is a conduit to Ruby's abductors since he witnessed it happen.
Later Kevin's code creates a huge image of Ruby's face. Kevin feels drawn to Okobogee again and Ruby is soon found in the woods comatose. She has a high white blood cell count, and symptoms of prolonged weightlessness that astronauts suffer from. When Ruby awakens she refuses to say what happened to her because "they" told her not to.
Scully listens to Mulder's hypnoregression by Dr. Werber about Samantha's abduction. Mulder feels paralyzed in bed and cannot move while Samantha is crying out for help. Mulder is not scared because of "the voice in my head" which tells him "Not to be afraid. It's telling me no harm will come to her, and that one day she'll return". Werber asks Mulder if he believes the voice, and Mulder says "I want to believe".

Plot Points:

UFOs have been spotted as early as 1967 in Okobogee Lake.
UFOs cause bright light and extremely high heat, enough to melt sand into glass.
A boy who witnesses an Okobogee abduction of his sister becomes a 'conduit', receiving information broadcasted from Earth satellites and the Voyager probe through binary code from TV static.
NSA was very concerned about the boy's code of a defense satellite.
The boy knows instictively when his sister is returned.
The sister was instructed by "them" not to say what happened to her.
During Samantha's abduction, Mulder is paralyzed in fear but a voice in his head calms him saying she will be returned.

Analysis:

In "One Son" we learn the Syndicate/Colonist alliance doesn't occur until '73 but the USAF has been flying UFOs since 1953 ("Dreamland") so this abduction could have been by the USAF or the Colonists. It is more likely the Colonists since though Syndicate UFOs are weightless the abductees only take a short flight on the UFO and spend most of their time in a Syndicate boxcar so would not have prolonged weightlessness. If it was the Colonists, why did they abduct her? She does not appear to be part of the Hybrid Program but she probably is anyway.
On the other hand another alien species has been shown that is not Colonist and not Rebel either; the Willowy Greys with the Whiteout powers. They appear in "Little Green Men" broadcasting the Voyager probe material as Kevin does in this episode; so perhaps Ruby was abducted by the Willowy Greys as preparation for their first contact with humanity, which ended up being Mulder who shot at them. They must have been disappointed!
The conduit ability never again appears in the series. Maybe it is because this an ability only of the Willowy Greys so most abductions (which are by the Syndicate and the Colonists) would not show this. Furthermore since Samantha was abducted by a Colonist UFO (as learned in "One Son") Mulder is not a conduit so he will not instictivly know when Samantha is returned nor will he start writing binary code suddenly.
NSA makes it first appearance in the series, afraid of an alien-touched boy knowing defense satellite transmissions. NSA later appears to be not part of the Syndicate and in fact an enemy of it. Defense satellites sound vaguely connected to the US military satellites in orbit in "Kill Switch" which fire deadly lazers.
If the abductors were the Willowy Greys, why would they tell Ruby to keep silent? They must want their arrival to be kept a secret until it happens. If otherwise, the ole coverup of the Hybrid Program.
Mulder was apparantly 'frozen' telepathically by the Colonist abductors, then spoken to telepathically by the Colonists, who showed pity on him and told him that Samantha would be returned, as per the Syndicate/Colonist agreement of 1973 shown in "One Son".

FALLEN ANGEL

The Run Down:

A 'Fallen Angel' craft is detected on the US electronic airspace fence and crashlands in Wisconsin. Col. Henderson from NORAD fudges the reports and calls someone to report a Fallen Angel and begin Operation Falcon. At the crash a police man is attacked by an invisable being which fires radiation.
Deep Throat informs Mulder, saying the electronic fence watches US airspace into orbit to track orbital satellites, and that Col Henderson leads Operation Falcon, he is the Air Force's best "reclamations" expert. During the Cold War his job was to prevent downed US jets from falling into Soviet hands. Mulder has 24 hours before the crashsite will be completely santized and any evidense removed.
Mulder infiltrates the quarantined lazer-fenced off area and reaches the crashsite. He sees a triangular UFO being covered with fire extinguishers from men in radiation suits before he is captured. In the brig he meets a UFO hunter from NICAP Max Fenig. Scully arrives to release Mulder. FBI Section Cheif McGrath of the Office of Personal Responsibility has overstepped Blevins to get Mulder kicked out of the FBI and the X-Files closed down over this. Scully was told the truth was a downed Libyan jet with a nuclear warhead.
Max ransacked Mulder's hotel room but is caught; he wanted to confirm Mulder's identity, NICAP has been following his career. Max has been monitoring radio waves, and heard the police man and later the med team being attacked by the invisable pilot. Max is on medications.
The invisable pilot breaks through the lazer-fence and flees the crashsite. Unaware, Henderson calls his superior to say "It will not get away. Not this time". The pilot emits an electronic transmission and Henderson tracks it down but the BlackOps teams sent in are irradiated by the pilot who escapes. Mulder asserts the pilot is firing intense ionizing radiation, which causes the severe burns all over the victims' bodies. Mulder calls it "close encounter mortalities" and says they are common in the X-Files.
Mulder finds Max having a seizure; Max says he is epiliptic since he was ten years old but he hasn't had a seizure in seven years because of his medication. As a kid he would wake up in strange places far away mysteriously. Max has a strange scar behind his ear, something he has seen before in two unconnected female abductees. Scully says Max is also taking anti-psychotic drugs. They later learn Max had a foreign object in his cerebellum.
Another larger craft appears on the US electronic fence, and hovers over Max's trailer in Wisconsin. Something intangible flies through the cieling of Max's trailer towards Max just as his ears bleed. Max then approaches the waterfront, and is intercepted by BlackOps troops. Max can talk but does not seem to have control of his body. The possessed Max irradiates the troops and moves on, followed by Mulder and Scully. Max waits in a warehouse in pain, saying "they" have come for him. Outside Henderson (with Scully captive) sees three infared images inside; Max, Mulder, and something else. The pilot batts Mulder aside, knocking him across the warehouse. Max is now being levitated in a bright light and sound while he convulses, until he disapeers in a flash of light. Now only Mulder is left.
McGrath grills Mulder and Scully. He has enough dirt to kick Mulder out of the FBI now, but he is countermanded by Deep Throat. McGrath asks why he ruined the best chance to get rid of Mulder. Deep Throat says Mulder's occaisonal insubordination is better "than having him exposed to the wrong people". Deep Throat thinks that Mulder doesn't have a clue to the truth, and says "always keep your friends close... but your enemies closer".

Plot Points:

NORAD runs an electronic surveillance fence that covers the US into orbit. It can detect UFOs.
Downed UFOs are called "Fallen Angels" and Col. Henderson of Operation Falcon are responsible for retreiving them. Within 24 hours of the crash there will be no evidense left of the crash.
This UFO was triangular and emitted radiation. The alien was invisable and could flash ionizing radiation. These aliens have come to Earth before and escaped the US's defenses.
Enter Max Fenig: repeated alien abductee who is abducted again in this episode by the pilot and its companions. He has a brain implant and suffers nose bleeds and seizures when his abductors are nearby.
The alien calls for a larger UFO which sends something to possess Max. The possessed Max can talk but has no bodily control and can rad-flash people without harm to him.
The aliens meet and teleport Max away.
OPR head McGrath is ready to fire Mulder but Deep Throat countermands him.
Deep Throat, as far as McGarth is concerned, is afraid of Mulder falling in with the wrong people. He knows Mulder isn't near the truth, and considers Mulder an enemy.

Analysis:

Though it is called a Fallen Angel the characters never actually say the UFO was shot down by the US, only that is crashed. It just mysteriously starts going crazy... apparantly just as it passes over West Virginia! In "Tempus Fugit"/"Max" we see the aliens who abduct Max are not Colonists since the military has no problem shooting them down. Apparantly the military and the Syndicate will try to shoot down any non-Colonist UFOs who enter orbit- is this a Colonist order to make sure they don't get any other options like the Rebels? So what downed this UFO? Was it some secret Syndicate and/or Colonist weapon kept in West Virgina? Maybe there was a Colonist UFO at West Virginia (since it is there where the Syndicate/Colonist alliance was struck) and it saw this intruder so it shot it down.
Henderson is most likely reporting to Cancer Man, or at least some Elder in the Syndicate.
This pilot is invisable, something we have never again seen except for maybe in "Fearful Symmetry" where aliens abduct zoo animals to preserve Earth's animals from extinction. This pilot also has rad-flashing ability, something seen in the Black Oil in "Piper Maru"/"Apocrypha" but that talent is never shown again. So what is it? The aliens who abduct Max are shown to be human sized Greys in "Tempus Fugit"/"Max", which is also what the USAF UFO pilots dress up as if you believe "Jose Chung". But it pretty much has to be a non-Colonist, most likely the Willowy Greys from "Conduit", "Little Green Men", and "Fearful Symmetry".
The UFO is also triangular, as is the Syndicate UFO in "Deep Throat", the Black Oil UFO in "Apocrypha", the Max-abductin' Greys in "Tempus Fugit", the Faceless Rebel Pilots' UFO and the Colonist UFO in "Patient X"/"The Red and the Black". This design seems to be what everyone uses pretty much so it doesn't particularly indicate anything.
Since the pilot is human shaped and very fast, it might by a Pilot, either a Facless Rebel or a Colonist-loyal solider.
Why cover the crashed UFO in fire extinguishers? To supress the radiation bleeding from the UFO.
McGrath goes over the head of Syndicate flunkie Blevins to kick Mulder out. Apparantly he isn't in regular contact with Syndicate officials so he only presumes their goals unlike Blevins who has direct orders on what to do with Mulder. McGrath's overeargerness forces Deep Throat as a Syndicate Elder to intervene, so that as part of Cancer Man's plan Mulder will continue to ridicule the truth seekers so people will not believe them until it is too late.
McGrath silently disapeers after this episode, though OPR appears regularly afterwards beginning in "Ascension" next season. Did the Syndicate remove him, discredit him, or kill him?
Henderson says it will not get away, not this time. This refers to a previous encounter where either the same alien nation intruded the US to abduct someone, maybe Max in peticular. So in a previous encounter the Max-abductin' UFO was able to escape, suggesting it can elude human defense system pretty well, supporting the theory that it was shot down this time only because a Colonist UFO happened to be in West Virginia on business with the Syndicate.
HUGE GAPING PLOT HOLE: If the BlackOps troops wore infared goggles they could see the pilot from a long ways away and kill him!
What is the pilot doing? He defends himself from threatening humans and flees the crashsite to elude Operation Falcon. He then emmits some kind of transmission, calling for help. Soon a larger UFO arrives and some kind of alien presence possesses Max, sending Max to a meeting with the downed pilot so the three of them can be safely transported to the larger UFO and whisked to safety. How can this UFO escape? Maybe the Colonist UFO has left Earth, or it cannot match this larger UFO.
So Max was first abducted at age ten and was taken regularly, causing him to have seizures when his abductors are nearby. He hasn't been abducted in seven years for some reason. Max has a brain implant, which seems a conceptual prototype to the neck implants first shown in "Duane Barry" which are Syndicate trademarks, like the implants in "The Pilot".
Max's possession is similar to the Black Oil in "Piper Maru"/"Apocrypha", except that Max retains control of his speech. Similarities; the possessor controls the body, can rad-flash people without harming the host body, and enters the body through an almost non-corporeal means. The Black Oil needed the oil as a medium, where this alien just flew in by itself.
So these aliens have teleportation abilites.
Who is Deep Throat afraid of Mulder allying with that is so dangerous? Obviously someone who would be able to reveal the truth to the general populace so they believe in the alien Colonization and the Syndicate collaboration. The Russian Syndicate who is fully aware of what is going on with the Syndicate and the Colonists? Then again this could just be Deep Throat blowing smoke up McGrath's ass in order to protect Mulder as his informant role and not as a loyal Syndicate Elder.
Deep Throat is right that Mulder doesn't have a clue to the truth. Mulder never even mentions the word "colonization" until "Colony", and then it doesn't appear again until "Talitha Cumi" then it doesn't appear again until "Patient X". He also doesn't have a clue about the Syndicate, about Cancer Man, about the collaboration, about the Hybrid Program, about the Black Oil, the bees, the smallpox programs, etc, etc, etc.
Deep Throat considers Mulder an enemy, at least this is what he says to McGrath.

EVE

The Run Down:

Twin girls are methodical murderers, and can telepathically communicate over large distances. They are clones of a clone Eve; one of the other adult Eves is insane and violent. These two are imprisoned with an insane older Eve who has been experimented on.
Deep Throat tells Mulder of the Lichfield Experiments in eugenics. "a group of genetically controlled children, raised and monitored" by the government. It was during the height of the Cold War when they learned the Russians were trying to use eugenics to crossbreed a supersolider so they started their own, highest level of classification, all records have since been destroyed. With an extra ten chromosomes, the Eves and Adams have heightened strength, intelligence, and psychosis.

Plot Points:

The government ran the Lichfield Experiment in eugenics, creating clones with extra chromosomes which gave them heightened strength, intelligence, but also psychosis.

Analysis:

This sounds like one of those pre-Colonist alliance Syndicate experiments in creating a supersolider to resist Colonization or an alien-human Hybrid. Since this project is so top secret, Syndicate involvement is a given. Plus, Deep Throat is so interconnected to the Experiment that he can get Mulder and Scully in to see the insane adult Eve in top security prison.
So Deep Throat gets Mulder and Scully in to a top security prison to see a top secret prisoner. How exactly can he do this without revealing the fact that he's an informant for Mulder? The answer is he can't! I'd say this proves that Deep Throat was not really an informant to Mulder (except for maybe in "The Erlenmeyer Flask") but a Syndicate plant.

CHANGE OF HEART

The Run Down:

A scientist discovers the secrets of anti-aging, and is making a deal with the US government for it. Mulder shoots him during a shootout. While dying Cancer Man is demanding where the scientist hid his information but the scientist dies. Mulder says he thinks Cancer Man is CIA to Scully in passing.

Analysis:

This is the first time Mulder sees Cancer Man (recently that is!) and he thinks he is CIA. They do not talk with each other.
This is just another example of the Syndicate generally looking for ways to strengthen humanity through genetic manipulation.

E.B.E.

The Run Down:

An Iraqi jet shoots down a UFO invisable to radar that attacks him somehow. The UFO crashes near a NATO base and as the troops move to the crashsite, a second UFO hovers overhead. A man drives a truck down a Tennessee highway when the radio goes crazy when reports of UFOs begin. The truck loses power and a circular UFO appears overhead. The driver gets out with a shotgun as the truck doors open by themselves. He fires his shotgun. The driver, Ranheim, has radiation burns consistant with Gulf War Syndrome but he claims to never have been in the Gulf War.
Mulder and Scully investigate the site; radiation five times normal, and 9 missing seconds at the site. Mulder says he's investigated sightings in Chesapeke Bay, Area 51, and Okobogee ("Conduit") but none have had this much supporting evidense: anecdotal data, exhume residue, radiation, missing time. Mulder asserts Gulf War Syndrome is from UFOs.
Scully's pen is bugged at a rental car agency.
Mulder introduces Scully to "The Lone Gunmen": a trio of paranoid conspriacy theorists who publish a newsletter and give Mulder information. Byers thinks the Russian communist leader is being put into power by CIA, looking for their old enemies again. They think a secret government really runs things. Metal strips in money track people. They don't think UFO cause GWS though. Scully later discovers the bug in her pen.
Mulder contacts Deep Throat by shining a light in his apartment, his response is a phone call of clicks. Deep Throat is afraid of a tourist taking pictures near him, and claims to be able to get seats to any sports event in the country. Mulder asks who is listening to them, Deep Throat only gives him a package and says he's on "a dangerous path". The package is the intercepted transcript of the Iraqi jet fight sent to "Commanding Officer, Majestric Project".
Scully finds that Ranheim is really Druse, Special Ops Black Beret in Iraq, he's had GWS for the past year. The truck he was driving was also much heavier than reported to be. Mulder asserts Druse is escorting the wreakage/pilots of the UFO crash to a US lab from Iraq. Scully asks about his source, Mulder only says he's guided them away from harm and he trusts them.
Mulder finds Deep Throat has broken into his department to give him another package that is too important to risk exposure by coming here. It's a photo of a UFO sighting in Georgia (while the truck is heading for Colorodo). Mulder takes the time to thank Deep Throat for his help, and Deep Throat looks ashamed when he leaves. Mulder thinks it is real but Scully disproves it. Deep Throat lied to him.
Mulder confronts Deep Throat, who says the photo "was prepared by our very best" but still claims to be an ally and says he puts in his life in great jepordy whenever they meet. He says he's been "a participant to some of the most insidious lies and witnesses to deeds that no crazed man could imagine. I spent years watching you from my lofty position to know you were the one I could trust". He lied to Mulder because "there are still some secrets that should remain secret, some truths that people are not just ready to know... the world's reaction to such knowledge would be far too dangerous". The Iraq jet transcript was truth to mislead Mulder from the truth. Deep Throat says Mulder must keep "swimming" to survive, that he isn't the bugger "but I do know they can still hear you".
Mulder ransacks his apartment and finds a bug in the power socket. Mulder and Scully then elude their trails and go after the truck which they have tracked down in Washington. They follow the truck for a long time then the radio goes crazy, hail falls, there is a loud sound and light and time seems to stop. Later they awaken to find the truck abandoned and an empty life-support unit inside. Mulder asserts they just saw a rescue operation. There was no missing time though; it was a hoax. Mulder asserts 'they' used sound weapons, stealth helicopters with an ultra-intensity light. They wonder why not just kill Mulder; maybe to use him to ridicule his crusade.
By contacting UFO watchdog groups who report an unprecedented number of sightings, they track the whatever to a power base called the "Northwest Facility" in Washington. They see Druse enter the base. The Lone Gunmen make fake ids for them to enter the base but they don't go to the highest security level (6). They are caught but Mulder runs into Level 6, avoiding troops. He reaches a huge room with a chamber in the middle where he is cornered. Deep Throat appears and orders away the troops.
Deep Throat says the alien is dead. After Roswell '47, there was an ultrasecret meeting between the US, Russia, China, UK, both Germanies, and France where it was agreed that if an EBE ever survives a crash, that country will be responsible for its immeadiate extermation. He claims to be one of three men to have exterminated an EBE. He was with the CIA in Vietnam, a UFO was sighted over Hanoi and the marines eventually shot it down "and brought it to us". Deep Throat wonders if it knew what a gun was but "the innocent and blank expression when I pulled the trigger has haunted me, until I found you." That's why he helps Mulder, to atone for that, and maybe someday through Mulder the truth will be known. Mulder isn't sure which of his lies to believe.

Plot Points:

A UFO attacks an Iraq jet and is invisable to radar yet is shot down by a missile. A second UFO watches the crash.
Something retreived from the wreakage is transported in a truck but intercepted by another UFO. This UFO/alien possesses telekinetic abilites to open the truck doors and causes crazy radios and power failure. It's aftereffects include radiation and missing time (9 seconds). The driver shoots something and survives.
The driver was a Special Ops Black Beret in Iraq and has Gulf War Syndrome; radiation burns. Mulder thinks UFOs cause GWS.
Both Mulder and Scully are being bugged. Deep Throat claims to know the bugger and that they can still hear.
Enter the Lone Gunmen: a trio of conspriacy theorists who technical abilites are of great help to Mulder.
When Mulder investigates the truck, Deep Throat tries to lure him away with doctored UFO pictures prepared by "our very best".
Deep Throat says there are some truths the world is just not ready to know, the world's reaction would be violent.
Deep Throat thinks Mulder will die if he stops his crusade.
Mulder and Scully witness a faux-UFO sighting; crazy radio, power failure, hail, bright light and sounds. No missing time. Mulder thinks it done with sound weapons and stealth helicopters with light weapons.
According to Deep Throat, Roswell '47 did happen. Because of it the major countries, communist and capitolist, all met and agreed to execute any EBEs who survive a crash.
Deep Throat claims to be one of three people in the world to have executed an EBE. It happened in Vietnam when he was with the CIA. The marines shot down a UFO and he killed it with a gun. It had an innocent, blank expression that haunted him.
Deep Throat claims to help Mulder as atonement, that he is in danger. He watched Mulder for years before deciding to choose him. He thinks that someday Mulder will reveal the whole truth.
Mulder is skeptical of anything Deep Throat says now that he has lied to him.

Analysis:

Whose UFO is shot down in Iraq? The pilot claims to be attacked (how he could survive a UFO attack is beyond me!) and Syndicate UFOs do not have weapons systems. We never learn if Willowy Grey UFOs have weapons systems. Of course, the Colonists or the Rebels would have little interest in Iraq (unless Hussein still has Black Cancer he alledgedly got from Russia which causes GWS). It is most likely a Syndicate UFO sent to spy on Iraq's defenses and the pilot was never attacked just approached.
How could a missile hit a radar invisable UFO? Heat-seeking! Since UFOs produce so much radation, it would a plumb target.
The alien UFO here causes missing time; 9 seconds. The Syndicate UFO in "The Pilot" causes 9 minutes, as do the Max-abductin' Greys' UFOs in "Tempus Fugit"/"Max".
This alien UFO was obviously trying to rescue the EBE inside the truck. It blows open the doors to get to it. So Druse shoots at...what? Shooting a UFO would do nothing of course, and Deep Throat later says it dead (though he could easily be lying). The most logical thing for Druse to shoot is the fallen EBE, thus depriving the UFO of what it wants and following the Cold War agreement. So for most of this episode, Mulder is chasing nothing and Druse is moving nothing. Druse actually driving off the UFO with a shotgun is just plain ridiculous, yet it does seem to support the facts.
The Iraq transcript is sent to Commanding Officer, Majestric Project. Deep Throat later says this evidense is true. So Majestric does exist (we see Area51 Men in Black are members of Majestric in "Dreamland"). Who is the CO? Is it a Syndicate Elder like Cancer Man?
Druse was obviously a Syndicate man, from the military special operations.
Deep Throat keeps Mulder from finding the truck, even through the alien is most likely gone (unless Druse was able to drive off the UFO with his shotgun!). This seems like true Syndicate work! Deep Throat is later killer but it is possible that he meets Mulder with the knowledge of the rest of the Elders as part of a way to control Mulder. Only when he exposes the most important artifact they have ("One Son") is he killed. Deep Throat also says the false photo was prepared by the best in the Syndicate, once again suggesting they know what he is doing. And if they know what he is doing, they must know Mulder has previously contacted him.
Who is bugging Mulder and Scully? Cancer Man! Deep Throat therefore says he knows Cancer Man in this episode, and is aware that Cancer Man still has surveillance on them.
Deep Throat knows there are secrets the world and Mulder is not ready for. This obviously refers to the colonization of Earth, the Syndicate collaboration, the Hybrid Program, etc. He thinks the world would react violently if they learned, most likely meaning they would rise up and kill the Syndicate!
The faux-UFO sighting; done with Syndicate UFOs or stealth helicopters. Since we see Syndicate UFOs have missing time abilites in "Dreamland" it must have been copters since the absence of missing time is what proves to Mulder that this is fake. Why not use a Syndicate UFO then? Writer's Problems....
Deep Throat says Roswell was real here, yet in "Erlenemeyer Flask" says Roswell was a smokescreen that they've had better salvage operations since then. Yet Cancer Man reveals Roswell really did happen in "One Son" so I guess Deep Throat actually was telling the truth!
The Cold War agreement is called Security Counsel Resolution 1013 by Deep Throat is the semi-fictional "Musings of Cancer Man" but it is never again referenced. It could be possible though, since the Syndicate didn't ally with the Colonists until 1973, desperate to survive that they would break this pact.
Deep Throat says he is only one of three, yet during the series we see several of Cancer Man's assassins killing off rebelling Hybrids left and right. This is most likely a lie. Plus, in the semi-fictional "Musings of Cancer Man" we see a similar incident in 1991 when Deep Throat executes a Grey recovered from a West Virginia crash. Which is truth, who knows?

TOOMS

The Run Down:

Scully makes an appearance before Assistant Director Walter Skinner (with Cancer Man watching in the background) who questions the work on the X-Files with its vague reports. Scully says they have an above-average case solving rate, and Skinner says that is the only thing that is saving them. At Cancer Man's silent urging, Skinner orders Scully to pursue conventional meathods, but Scully protests saying that will decrease their case solving rate.
After being framed by a mutant for beating him, Mulder (and Scully) are called before Skinner (with Cancer Man watching in the background). Skinner tells Mulder his talents are being wasted on X-Files, advises him to step away. At Cancer Man's silent urging Skinner forbids Mulder from being near the mutant. Cancer Man walks near Skinner, who then says Mulder was close to being kicked off no matter how many Congressional friends he has.
After killing the mutant, Skinner asks Cancer Man if he's read the report, if he believes it. Cancer Man says "Of course I do".

Plot Points:

Enter Assistant Director Skinner, who appears to be a pawn of Cancer Man and is skeptical of Mulder's beliefs.
Cancer Man believes Mulder's crazy reports of unexplained phenomena.

Analysis:

This is the first time we hear Cancer Man talk. This is the first time Mulder sees Cancer Man in a position of power in the FBI, and second time for Scully (first in "The Pilot"). Considering Mulder thought him CIA in "Change of Heart", Mulder be very suspicious to see him in Skinner's office urging Skinner on!
Skinner is subtly shown here to be following Cancer Man's orders against his better judgement, but his true feelings come out when he speaks about Mulder's talents being wasted.
Considering all the aliens that Cancer Man has seen, it's no wonder he believes in unexplainable phenomena, but more importantly he believes it because Mulder says it not because he accepts the possibility.

THE ERLENMEYER FLASK

The Run Down:

Police chase a man with superstrength who shrugs off tazers. He is shot and jumps into the harbor, bleeding green blood.
Deep Throat calls Mulder in but refuses to give any information. Mulder and Scully eventually find the man was driving the car of a Doctor Berube. Berube refuses to answer their questions, he is working on a experiment with monkeys. Scully criticizes Deep Throat, and Deep Throat later visits Mulder because Mulder is giving up to easily. Deep Throat says he can't tell him anymore, but Mulder has never been closer to the truth before. Deep Throat fears Mulder has become too dependant on him.
The man Secare can breathe underwater and has been hiding in the harbor. Crew-Cut Man, who was earlier investigating Secare, questions Berube about being in contact with him. Crew-Cut Man says his work is done and kills him, making it look like a suicide. Berube was working on the Human Genome project to map all human genes, the most ambitious scientfic project ever. Berube had an erlenmeyer flask labelled "Purity Control" holding a red liquid.
Scully has the red liquid analyzed. It is the size of bacteria but is not structured the way bacteria is. It is green and each contains a virus in it. Berube was trying to clone it. They resemble cholorplasts/plant cells. Cloning the virus in the bacteria and injecting it into something living is called gene therapy. Mulder asserts Berube was doing this with the monkeys. Such bacteria has not existed on earth for millions of years, before fish crawled out of the sea. DNA tests of the bacteria finds a new base pair of genes/nucleotides, which are by definition extraterrestial.
Mulder searches Berube's house and gets a call from Secare while being listened in on by Crew-Cut Man. Secare collaspses and is taken onto an ambulence. When they ventilate his lungs, something is released that injures the meds. Secare runs off.
Mulder finds Zeus Storage. Inside one room is six green tanks being monitored by computer, five of the tanks have humans inside, who are alive and breathing underwater. Mulder is chased off by Crew-Cut Man and a group of men. He returns with Scully the next day to find the tanks and people gone.
Deep Throat arrives to say they've been most likely destroyed, by who he doesn't know. Mulder doesn't believe him, but Deep Throat says there are limits to his knowledge. There are black organizations that operate inside the intelligence community unbeknownst to others conducting covert activites. Deep Throat says the men who chased Mulder are trained very well for assassination so they let him go. Mulder asserts Berube was conducting human experiments with exterrestial viruses. Deep Throat says "yes but that's been going on for years. We've had the tissue since 1947 but not the technology. Roswell was a smokescreen we've had half a dozen better salvage operations." Berube was killed because his work was too successful, it was in this room "where the first DNA transplant took, the first human-alien hybrid was created". Berube's experiment was with six terminally ill volunteers, one of whom was Berube's old friend Secare. "As a result of the E.T. gene therapy" all six recovered from their illnesses but also devealoped superstrength and the ability to breath underwater, and have a blood chemistry that is alien "and very likely toxic". Berube's experiment was part of a "top secret government project being run out of Los Alamos. All they were interested in was the technology, not the science." Secare and rest were supposed to be killed, alive they are a liability, but Berube warned Secare. Scully asks why he is giving so much now, Deep Throat says he didn't antipate the speed and precision of the clean-up operation. He says they must find Secare before they do or they'll have no case, he will have no further contact with them on the matter.
Mulder finds Secare at Berube's house but Crew-Cut Man arrives wearing a gas mask. He shoots Secare in the back of the neck, which causes Mulder to be infected by the now-airborne alien retrovirus. Secare is later dead and Mulder's face is severelly inflammed. Crew-Cut Man is holding Mulder prisoner.
Scully learns the doctor she was working with was killed, her bacteria sample was taken, and Mulder has disappeared. Deep Throat contacts her, concerned about Mulder. He knows they won't kill him, because he is too high profile and can expose them, he tells Scully. Deep Throat says evidense still exists, and with Scully's medical background he can get her into the Fort Marlene high containment facility in Maryland where they have "the wellspring, the original tissue." If they have Mulder they would be willing to deal for it and save his life. Using Deep Throat's faked credentials Scully reaches the top level of Fort Marlene, the Cryology division. She guesses the project password "Purity Control" and gets the small alien fetus kept in a liquid nitrogen container.
Scully later meets Deep Throat with the alien fetus. Deep Throat says they're willing to make the exchange, Scully questions the fact that he spoke to them. She refuses to hand over the fetus, Deep Throat says they're expecting him to make the deal. Deep Throat says in 1987 a group of children in a southern state were injected with cloned DNA fetus instead of a routine innoculation. That is the kind of people they are dealing with. Scully questions giving it back to them, Deep Throat says Mulder is needed to expose everything this is just the tip of the iceberg. Scully reluctantly hands over the fetus as Crew-Cut Man arrives. Deep Throat gives Crew-Cut Man the fetus and then Crew-Cut Man shoots him. Mulder is thrown out and Crew-Cut Man drives off. Scully runs to Deep Throat, who tells her "Trust No One" and then dies.
Two weeks later Mulder calls Scully. The X-Files are being shut down and they are being seperated and re-assigned. Mulder heard from Skinner, who said word came down from the top of the executive branch.
Cancer Man puts the alien fetus into a evidense drawer holding several others in the Pentagon Security Vault.

Plot Points:

A Syndicate doctor Berube created Weak Hybrids, the first Hybrids to have succeeded. These are ill humans given E.T. gene therapy (injected with the alien bacteria and virus). Their abilites: green blood, non-leathal alien retrovirus when bled, superstrength, ability to breath underwater.
Berube worked from Purity Control, taken from "the wellspring", an alien fetus. It is a plant-like alien bacteria with an alien virus within it. The bacteria is by definition extraterrestial since it hasn't existed on Earth since the fish crawled out of the sea.
Crew-Cut Man, a Syndicate assassin, kills Berube for exposing the experiment and kills the test subjects.
Deep Throat brings Mulder on to the case but is reluctant to give information until later.
According to Deep Throat, human experiments with E.T. viruses have been going on for years.
According to Deep Throat, Roswell gave them the tissue but not the technology. There have been @6 better salvages since then.
Mulder is taken captive by Crew-Cut Man and infected with the non-leathal alien retrovirus.
Deep Throat gets Scully to steal "the wellspring", an alien fetus, from Fort Marlene to exchange for Mulder.
Crew-Cut Man kills Deep Throat in the exchange. Deep Throat dies telling Scully "Trust No One".
The X-Files have been closed and Mulder and Scully will be seperated. The order came from high up, Skinner had no choice.
Cancer Man puts the retreived alien fetus in the Pentagon Storage Vault.

Analysis:

So the Berube Hybrids are humans injected with the Alien DNA. They are Weak Hybrids: green blood, a weak alien retrovirus in the blood that does not kill when exposed to air, superstrength, ability to breath underwater. They are the first Hybrids to have taken, ie the first to accept the operation and survive. Note that Crew-Cut Man shoots Secare in the back of the neck; perhaps Weak Hybrids can be killed by gunshot but only in the back of the neck, where all Hybrids and Pilots have a weakness. This shows of course that this Alien DNA comes from the Pilots, yet Deep Throat claims this DNA came from the Grey looking fetus. Greys are not Pilots are far as we can tell. Since Rebel Pilots (who do not have Purity/Black Oil in them) probably can not morph (see conflicting evidense in "Two Fathers"/"One Son"), it can generally assumed this is an ability that comes from the Colonists' genetic improvement of the Pilot species. So why does a Grey fetus have Pilot abilities? Pilots and Colonists have been pretty much shown to be seperate species, unless the Pilot genetic improvements by the Colonists are their own abilites lent out.
Was Berube injecting the monkeys with Alien DNA? The monkeys were alledgedly vicious but why would he bother with monkeys when he is injecting humans? If they were prototypes/test subjects why haven't they been killed yet?
The breathing underwater thing kinda comes out of left field. Why can aliens breathe underwater? Is their planet underwater or something? This ability is never really mentioned again in the series.
Why in the world would Crew-Cut Man kill Berube but leave the Purity Control sample for Scully to find?! Didn't he check the lab for vitally important things like this, even if he didn't know of it ahead of time.
So Alien DNA resembles plant life. What does this mean?
Notice how the Purity Control sample has plant-like bacteria with a virus inside. Notice how all along Scully is testing the bacteria and not the virus. The bacteria is the alien tissue, the virus is... Purity! The Black Oil! The Colonists! The bacteria is just whatever alien body the Purity was inhabiting, namely that of a Grey fetus. Good thing Scully never looked at the virus, or she would be about five years ahead of the series' progression! This episode really did feature extreme foreknowledge of the future arc; the Black Oil appears here! The way the virus is stuck to bacteria even shows the way Purity is infecting all species in the galaxy trying to acheieve racial 'purity' for the galaxy.
So Greys might have been just another race Purity has taken over, yet this is the form they take most of the time. That, and the Pilots.
Berube was cloning the Purity and then injecting it into humans. But the alien bacteria was also going in, so that is where these traits are coming from, the superstrength and alien retrovirus. But apparantly the Syndicate's objective in this Hybrid Program is to create a 'true' Hybrid, whatever that means. Perhaps a 'true' Hybrid means a human with Purity abilities, so Berube is doing gene therapy trying to transplant the Purity DNA but instead is only transplanting the Alien/Grey DNA. That's why this Hybrid experiment fails. So maybe this means Cassandra Spender as a 'true' Hybrid has Purity DNA within her. Considering that all humans have latent Purity DNA already ("The Beginning") it would seem more like a matter of re-activating it rather than introducing it to humans.
The alien bacteria has not existed on Earth for millions of years, before fish crawled out of the sea. In The Movie Well-Manicured Man tells Mulder that Purity was the first intelligent form of life on Earth and walked the earth before the dinosaurs. This connects the Grey/alien bacteria back with Purity again, which is a problem. Perhaps the Greys visited Earth back then only to be taken over by Purity, which then began its mission of interstellar genetic conquest with the Greys as its first victim.
So none of the humans exposed to the alien retrovirus when Secare is bled are killed, just inflammed in the face. This shows that this is a much weaker version of the alien retrovirus in the Pilots (first seen in "Colony") which can kill a human.
Is the green water of the Hybrid tank significant? Green tanks where Hybrids are grown/kept appear again in "Colony"/"End Game" and later in "Memento Mori", both of which are Clone Hybrids growing more Clone Hybrids.
Deep Throat says if Crew-Cut Man wanted Mulder dead he would be dead. Why wouldn't he? Because Crew-Cut Man is a minion of Cancer Man, who has standing orders to let Mulder live. Not only because Mulder poisons his own crusade, but because of Cancer Man's personal feelings towards Mulder who is his pseudo-son.
Deep Throat is definitely lying again to Mulder at Zeus Storage. He very definitely knows who is running the clean-up operation, Cancer Man, who we later see is a close friend of Deep Throat's. Though Deep Throat maybe in charge of political subversion in DC and Cancer Man runs the Hybrid Program and clean-up/assassination crews, they still knew each other.
Deep Throat admits that human experiments with E.T. viruses have been going on for years, beginning in 1973 presumably ("One Son") when the Syndicate-Colonist alliance is struck. E.T. viruses of course refers to Purity.
Deep Throat is definitely lying when he says that since Roswell they've had the tissue but not the technology. In fact after Roswell they had the technology but not the tissue! Thanks to Roswell and other salvage operations, the Syndicate is able to use UFO tech to fly their own UFOs beginning in 1953, 19 years before they ally with the Colonists. And they allied with the Colonists in order to get access to the alien DNA/tissue. So even here Deep Throat is still keeping the greatest secrets of the Syndicate from Mulder, once again proving that his duplicity is more against Mulder than it is against the Syndicate.
It is curious how vocal Deep Throat suddenly gets. Most likely he has now conferred with his other Syndicate Elders and they have decided what to tell Mulder to mislead him, but when he first warns Mulder he says nothing because he has not conferred with the others and so does not know what is safe to reveal/lie about.
Notice Deep Throat says Berube was killed because his work was too successful. This stretches forward to "One Son" where we learn the Syndicate never wanted to succeed in the Hybrid Program just play for time, and to kill any 'true' Hybrids they make.
Of course, Deep Throat having the alien fetus stolen has to be an act against the Syndicate's best wishes. Though Scully never really knew what she had, (and we never really knew either until "One Son"), it was the worst possible thing to expose them too. Perhaps Deep Throat thought it would allright because Mulder and Scully would never really know what they had so briefly, or he was trying to negotiate with the more aggressive members of the Syndicate (ie Cancer Man), but this was the last straw for them. It is highly unlikely that Deep Throat was a true informant all this time and that only now did the Syndicate realize his duplicity. For example, how could he get the Syndicate to make up a fake UFO pic for Mulder in "E.B.E." if they didn't know? There are just too many instances of exposure.
The project password to the alien fetus was 'Purity Control'. This refers to Purity/the Black Oil/the Colonists, showing the Syndicate is really looking for a way to CONTROL the PURITY, ie find a vaccine for Purity to defeat the colonization.
That little factoid about the 1987 innoculation sounds like some bull Deep Throat made up on cue to sway Scully.
Cancer Man ordered Deep Throat killed for stealing the alien fetus. Crew-Cut Man followed his orders and released Mulder as per Cancer Man's ongoing orders.
Now that Deep Throat is dead, who will replace him as a Syndicate Elder responsible for the political situation in DC?
Cancer Man also has the X-Files closed and Mulder seperated from Scully. Perhaps when Scully got the alien fetus he realized that Mulder and Scully were getting out of hand so they had to slapped down for awhile.
Why does Cancer Man put the alien fetus in the Pentagon Storage Vault? Doesn't it have to be in liquid nitrogen, and besides when next we see it it's back in Fort Marlene in "One Son"!

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