A Roush Technologies employee is infected with the Black Oil virus and the newborn creature that gestates is on the loose. The Cigarette-Smoking Man uses Gibson Praise to hunt it. The X-Files reopen, but with Diana Fowley and Jeffrey Spender on the job. Scully uncovers evidence of the presence of the virus' DNA in every human's DNA, possibly making everyone part extraterrestrial. The creature sheds its skin and turns into a grey alien.
The end and the beginning. The X-Files leave Vancouver and move production to Los Angeles, and it shows from the first frame: a big shiny sun! This is the first of the signs that this season will take a much different path from the 'classic' XF of the Vancouver era: there will be many more 'light' stories this year, much more humor (not always for the best) and the general gloomy atmosphere, despite LA's quality work, is gone. The Beginning, written by Carter, continues the story of 5X20: The End and close some threads Fight the Future left hanging.
The X-Files office v2.0
With this closure and reopening of the X-Files, Carter does not repeat what had happened between 1X23: The Erlenmeyer Flask and 2X06: Ascension. Mulder and Scully are reassigned on the long term, while their positions in the X-Files are filled by agents Fowley and Spender, a most unlikely duo. The beginning of the episode is spent summarizing the events of the season finale and the movie in the most obvious manner. Mulder is so obsessed that he hopes to restore the hundreds of burnt pages of his precious files fragment by fragment (ah, the remote time when no digital copies in safeguarded servers existed anywhere). This is a noble enterprise, but of which Mulder is tired. As Skinner says, "When will you accept that no amount of pressure or reason will bring to heel a conspiracy whose members walk these halls with absolute impunity?" Scully, being unnervingly muleheaded, still doesn't believe Mulder's theories despite her experience in the movie; she needs the theories to be baked up by science. By the end of the episode, the evidence she herself uncovers is a sign of hope that exposure might really possible.
And who better to accompany Spender in his arrival in the X-Files but the woman who had accompanied Mulder the first time? Diana Fowley had also joined the X-Files back at the time at the request of the CSM (but that only becomes clear in 6X12: One Son). We learn than not only had they worked together on the X-Files in 1990-1991, but that "you and I found the X-Files together". The mystery remains on what happened in the 1992-1993 period (between the 1X79: Pilot and 1X01: Deep Throat), a blatant inconsistency from Carter. Mulder and Fowley are partnered once again just for this episode. Scully has many suspicions on Diana, but Mulder still trusts her blindly ("Agent Fowley took me to that plant at great risk to herself"). Scully finds her report conveniently silences many substancial points. Mulder justifies this by saying "Agent Fowley's report was a means to an end. Trying to protect the work. Protect the X-Files". An all-out report at such a sensitive time would have had the same disbelieving and dismissing reception as Mulder's report in the beginning of the episode, and would have led to closing the X-Files once again. Indeed Fowley never straight out lies to Mulder either: "I was given this assignment, Fox, OK? They offered it to me. I took the chance." and this is completely true, she is very good at playing double agents for the CSM. However, with Fowley replacing Mulder on the X-Files, Mulder cannot but feel a bit betrayed, and perhaps even suspicious: Mulder: "Who sent you?" Fowley: "I'm here on my own."
In the case investigated here, it's Skinner, the middle man between Spender and the CSM, who tips the case to Mulder; Skinner is yet again in the middle of a difficult situation but still finds ways to help Mulder's quest. Muder and Scully investigate this case outside of their jurisdiction, unofficially (notice the civilian clothes). This forces the Office of Professional Review (the same OPR from the movie?) to distance Mulder & Scully from the X-Files for good and place them under a different Assistant Director: the bleak Alvin Kersh. Spender and Fowley install themselves in the X-Files office. The "I Want To Believe" poster is replaced by a politically correct picture of President Clinton, and to underline Scully's unfair treatment both new agents will soon have nameplates on the door!
Roush Technologies and the Black Oil alien life cycle
Sandy, the scientist who got infected with the Black Oil virus, was working for Roush Technologies (seen on the company van that takes him home). The (only) other time we heard about Roush was in 5X03: Redux II: it's the biotechnology firm the Syndicate uses as a front. Given the way the Black Oil virus acted on Sandy, Roush must have been working on the Black Oil uncovered in Blackwood, Texas (Fight the Future), working on a vaccine.
The alien "creature" gestates and is 'born' very quickly ("just 12 hours"), probably because of the heat he was bred in -- contrary to the creature in Fight the Future, whose development was slowed down by turning the temperature close to freezing. 'It' leaves Sandy's house and wanders the desert in search of a source of heat ("It wants heat. It needs heat."). Heat, as a source of energy, helps its development, just like a cold-blooded reptile thrives in warm climates but doesn't survive in cooler areas of the world. It finds heat inside a nuclear power plant and kills one of the employees there (named Homer...Simpson?). It seems to change skin a first time (the big slimy chunk of organic material Mulder and Fowley find). After killing the CSM's henchman who was with Gibson, the creature moves further inside the nuclear plant, into the pool just above the core of the nuclear reactor, among the rods controlling the nuclear fuel. On a side note, because of extreme safety procedures related to radiation exposure in the core, there is no way that anyone, be it the creature or Gibson and the man, would have got in there without being noticed! As established in 3X15: Piper Maru, the Black Oil doesn't fear radiation. And in the pool, the creature alien sheds its skin again, and reveals a grey alien, the mature form of the Black Oil alien race and the final stage in its evolution. The creature form only insures the survival of the alien at first; the grey is weak and fragile but it's the form under which this race can develop a social life, technology and civilization.
Gibson Praise and the genetic link
The CSM uses Gibson Praise's mental powers to locate and exterminate the creature alien. Ever since Gibson came in the hands of the Syndicate, they have been trying to understand how Gibson got his special powers. At the end, Gibson and the creature seem to communicate telepathically, since the creature spares Gibson's life. Scully has the chance to examine Gibson again after The End using what she learned in Fight the Future. Despite Mulder's initial claims, Scully has found that "that virus' DNA and proteins are very much of this world"; no direct examination of the virus can prove its extraterrestrial origin (unlike the examination of the green toxin in 1X23: The Erlenmeyer Flask), it is 'only' a new kind of virus. At first, Scully finds "evidence of the virus in [Gibson's] system", which establishes "a link" between his abilities and the Black Oil virus. Further tests prove that "DNA from the claw nail we found matching exactly the DNA from the virus you believe is extraterrestrial. [...] Which matches exactly DNA that was found in Gibson Praise. [...] It's a part of his DNA." This echoes what was only suspected in The End, that "Gibson is in some part extraterrestrial." Only that this part of virus DNA is "a part of all of our DNA. It's called a genetic remnant. It's inactive junk DNA. Except in Gibson it's turned on." The 'junk' DNA in a common human is inactive.
But what use is the Black Oil genetic material in our DNA? Scully's study of the virus concludes that "it attacks and destroys human cells but that is all it does, Mulder. It creates nothing"; nothing that would trigger the gestation of something as complex as an entire alien creature. The answer may be found in that the virus' genome does not contain all the information necessary for creating a creature or grey: the Black Oil virus only contains what is necessary for its survival and its sentience, nothing more. The virus then recognizes the alien parts of the human host's DNA and uses them in order to start the gestation. The gestation is impossible with the virus only, it needs the human host as more than food but as an 'external information tank' to be used when necessary. The Black Oil combined with human DNA permits the development of a grey alien. This information was put there on purpose for the future date of colonization, back when humans were designed by the Colonists, something that will be fully explained in 6X22: Biogenesis. This explanation reconciles the persistant naming of the Black Oil as a "virus" with the fact that a virus is much simpler than a complex organism as a grey. Information on this was found in the book by Anne Simon (Carter's scientific advisor on The X-Files)!
Scully: "I know that you don't want to hear it -- not that you can't question me and what I saw -- but what you can't question is the science."
Cigarette-Smoking Man: "Never underestimate the public's willingness to blame the Red Man for... anything they can't explain."
Gibson Praise (to Scully): "You just don't want to believe it."
Cigarette-Smoking Man: "You did well, son. He's on very thin ice now, you know?"
Spender: "Mulder will be back. As long as he lives, he won't give up."
Cigarette-Smoking Man: "Well, there's solutions, of course. Simple but extreme solutions. I've used these methods. They have their place. But not here."
Spender: "You've killed men?"
Cigarette-Smoking Man: "You can kill a man but you can't kill what he stands for. Not unless you first break his spirit. That's a beautiful thing to see."
Mulder: "So if that were true, that would mean that Gibson is in some part extraterrestrial."
Scully: "It would mean that all of us are."