Seven years after their first case together, Mulder and Scully are brought back to Bellefleur, Oregon. A UFO has crashed; the dying Cigarette-Smoking Man sends Krycek to recover it in order to rebuild the Project, but the ship rebuilds itself. The Alien Bounty Hunter collects all the abductees, cleaning up evidence and still preparing the colonization. Under the eyes of Skinner, Mulder is abducted by the ship. Krycek and Marita push the Cigarette-Smoking Man down the stairs, possibly killing him. Scully is pregnant. Wow.
Mulder: "It has to end sometime. That time is now." Written by Chris Carter, Requiem was to be the series finale had the X-Files not been renewed at the last minute for another season -- the announcement came just one week before the airing, which in TV production terms is nothing. Few changes were made to the episode after it was known that this was not the end. We still don't know what an alternative finale would have shown exactly (early spoilers talk of a scene in the alien ship with Mulder seeing a man who calls himself his father, but W.B.Davis has denied this as fake). This is the end of the Mulder & Scully era, and for me the point where the series should have ended its course. There is no "To Be Continued" mention, further separating Requiem from the season 8 openers 8X01: Within & 8X02: Without. Requiem does not actually offer much in terms of mythology elements -- after all much of the mythology is over since 6X12: One Son -- but it still stands as an open-ended finale without having to refer to seasons 8 & 9 for answers. This is a closure episode: paths past are considered and reviewed, and destinies future are forged. It's not the perfect ending for a series like the X-Files, it leaves many threads open, but so would any kind of finale -- after all, life goes on even after a series finale (see JM Starczynski's magnificent "Babylon 5" (1993-1998) for example). Requiem actually does not stand to the heights of other great episodes of the series, it's not the multi-part series finale we were promised, but it's what we got, and it will do.
Abductions: it's happening again
The abductions start again in Bellefleur, Oregon. This time it's different: this is not a single random abductee being taken for 'routine' tests, all of the Bellefleur abductees are "systematically being taken". Not all abductees are taken though: Scully is 'rejected' by the force field that acts as a security filter, whilst Mulder is accepted. Scully finds that the Bellefleur abductees experienced "anomalous brain activity", "electro-encephalitic trauma", "which is exactly what Mulder experienced earlier this year" (see his instantaneous conversion to a hybrid in 7X04: Amor Fati). Scully is an abductee that went through none of that; very different hybridization experiments were conducted on her, but after she healed, no genetic evidence remains on her whatsoever -- she's just carrying implants. Another reason why Scully is not taken is because she's pregnant with a very important being for the Colonists (see 8X21: Existence).
The abductions take place to remove all living proof of alien experiments and alien presence on Earth, taking all the persons that through their past abductions or genetic profile could have been turned into hybrids easily (something that will be confirmed in 8X01: Within). On a side note, in the photos of the scars and implant marks left from the abductions in the medical records of Ray Hoese we can clearly see a scar mark behind his ear: exatly the same scar as multiple abductee Max Fenig in 1X09: Fallen Angel!
Bellefleur seems to be one of those "alien Lighthouses" Krycek was talking about in 5X14: The Red and the Black: places of intense alien activity where abductees are gathered and taken. Mulder discovers his very own mark, the red 'X marks the spot' on the ground, in the same place where there is still an alien presence 7 years later; obviously this is an alien hotspot. The Cigarette-Smoking Man says that the UFO that crashed is "rebuilding itself": evidently some nanotechnology is at work here (the one from which the nanotechnology in 6X10: S.R.819 is derived from?); the same thing must have happened with the Ship in 7X03: The Sixth Extinction, the Ship repairing itself until it took off and vanished. The CSM further reinforces that aliens-God link: "There's no God, Marita. What we call God is only alien, an intelligence much greater than us." As with the Ship in The Sixth Extinction, the CSM says about the ship in Requiem that "to possess it is to possess the answer to all things, every possible imaginable question".
Rebuild the Project?
Krycek is liberated from the Forj Sidi Toui Penal Colony in Tunisia. As with any Tunisia reference since Fight the Future, this should not be overlooked. This comes as an indirect confirmation that Conrad Strughold is still alive and in contact with the CSM, and they have enough interests to protect so as to get rid of any enemies like Krycek. Krycek was incarcerated "for trying to sell something that was mine", most likely the data around the artifacts of 6X22: Biogenesis and perhaps the artifacts themselves. As in 3X15: Piper Maru, Krycek tries to survive on his own by selling information to the highest bidder. Last time we saw Marita Covarrubias was in 6X12: One Son, in a pretty bad shape from the experiments done on her for the vaccine against the Black Oil. Krycek says "The last time I saw you, I left you for dead."; even if it's not clear, perhaps she was dying from the experiments; after the Syndicate's demise, the CSM must have cured her (with the vaccine or the chip of 7X15: En Ami) and as she regained her strengths, he must have taken her under his wing.
The Cigarette-Smoking Man still smokes cigarettes, despite his advanced terminal illness, pathetically puffing through a tracheotomy. He lives in an apartment of the Watergate complex (it doesn't look like Diana Fowley's apartment from One Son), taken care of by his nurse Greta. "His last wish is to rebuild his Project, to have us revive the conspiracy." Even if he's dying, he still believes cooperation with the Colonists is the way to the salvation of Mankind (part of it anyway). An event like that of 4X17: Tempus Fugit occurs: "There's been a crash in Oregon. An alien ship has collided with a military aircraft." The military still hunts down UFOs according to UN Resolution 10.13 (1X16: E.B.E.). "The Navy found their plane about three miles away"; the alien ship is invisible, "hidden in plain sight", "cloaked in an energy field", the same field that lets specific persons go through it. "It's Roswell and Corona all over again, 50 years later." The town of Corona is actually closer than Roswell to where the alleged crash occured, but Roswell got all the credit. The CSM hopes to reclaim the ship and perhaps use it as a bargaining item over which to conclude another agreement with the alien Colonists. Indeed, everything that happens in Bellefleur is done directly by the Colonists, by their field task force the Alien Bounty Hunter: "[he] mops up the evidence [...] he's eliminating proof of all the tests" (Krycek). No human interference here. After the end of the Syndicate, the Colonists completely ignore the humans and continue their business of preparing the ground for colonization on their own.
The CSM brings Krycek and Marita together as the seeds of a potential new Syndicate; the lack of trust is mutual ("Do you trust Alex, Marita?") and the grudges the ex-lovers hold against the CSM run deep. Krycek does not find the ship in time; the ship takes off and the chance to rebuild the Project is gone. The CSM brought his own nemesis upon him. Krycek, with Marita at his side, sends the CSM tumbling down the stairs; the fall looks lethal, especially for somebody as weakened as the CSM. Even if he's not dead, their point is made: the CSM is nothing, Alex and Marita are in power now. Krycek never believed in the agreement with the Colonists, he has been a supporter of resistance -- hence the CSM's comment "perhaps you never meant to succeed". It's likely that the two ex-lovers will form a core of resistance, an anti-Syndicate that will lead the effort against colonization. (An alliance between Krycek and Covarrubias, the alien Rebels and the Russian conspiracy around the Biogenesis arifacts was at the heart of would-be season 7 mythology episodes. It's a shame these never got made...) The CSM's last words are a plea for reconsidering cooperation with the Colonists: "As you do to Mulder and to me, you do to all of mankind"; for the CSM, resistance is equivalent to defeat and death. At the end of 7 years of mythology, the future is pretty grim. The colonization is still actively prepared by the Colonists, leading to an inevitable doom for mankind; any resistance looks quite weak and does not look as if it has the tools that it takes to succeed against such an impossible enemy.
Beliefs shaken and destinies made
The finale brings our two agents back to the place of their first case 7 years ago (1X79: Pilot), back in Bellefleur, Oregon. Much has changed in Bellefleur since the last time Mulder & Scully were there: Billy Miles got married, divorced, got a job in law enforcement; Teresa Hoese got married and became a mom... These changes are reflected in the way the Mulder-Scully relationship has evolved since then. Evidently Mulder and Scully form a couple, flirting more and more openly since season 6 and firmly together since sometime around 7X17: all things -- the evolution of their relationship has certainly been towards a romantic involvement, but the writers have cared not to put it on the focus of the series, as was promised in the earlier years.
After 7 long years of partnership with a believer, Scully's sceptic bases have somehow given ground to a more open view to the world; she still needs facts to believe, but she has seen enough so as not to dismiss more extreme possibilities. "I've seen things that I cannot deny." The budgetary review the X-Files go through in the beginning of the episode serves as a mirror to how far the two agents have come -- also hinting that the X-Files would be shot down once again, this time for good. Mulder is no longer the lone 'Spooky' that believes in aliens, there's Scully with him ("[a toxin] from what is arguably an alien"). Skinner too, the torn and ever-present companion, has seen enough to make him a believer as well; and this time he won't hide the truth for the sake of conventional belief in the FBI or because the CSM ordered him to do so, as was the case in the past: "I'll be asked what I saw. And what I saw, I can't deny. I won't."
As for Mulder, he finally touches the truth he's been seeking for all these years: he reaches the aliens, and like his sister so long ago he is abducted. Mulder's quest for this form of God has always superseded any cost that would go along with it; he disregards completely any physical pain that might result from the tests, he just wants to 'touch God' (already in 2X05: Duane Barry he begs "Let the others go and take me"). His wish is granted here, taking him to places unknown and a future uncertain. Had this been the end of the series, there's nothing that prevents us to suppose that Mulder would have been returned and taken again and again, a multiple abductee like many others (since the Supersoldier thread is not introduced yet). The Mulder-Scully separation could have been only temporary, and the abduction being there to fulfill Mulder's character arc. But as the budgetary review scenes suggest, the time has come for both of them to move on with their lives, away from the X-Files and away from the FBI. To enjoy their lives while they can, before colonization. A rather grim ending; but real life, like the lives of Mulder & Scully, is a constant struggle with some moments of happiness with no other end in sight but death.
All the surviving characters are brought together. This is best illustrated by the famous 'Last Supper' scene in Skinner's office, inspired by Leonardo Da Vinci's famous painting, with Mulder serving as Christ (as he is about to be abducted, to ascend), and prehaps with Krycek as Judas (and fast food and coke as bread and wine! America, fuck yeah!). By touching on every character's destiny and bringing them on one kind of conclusion or another, a chapter in the lives of the people we have followed throughout the series is closed.
Fade to black.
Special Agent Chesty Short: "Investigating your sister's abduction and the government conspiracy around it. Both of which have been resolved, correct?"
Mulder: "Nothing has been resolved exactly."
Scully: "I believe that there was once a conspiracy. I believe I was taken by men who subjected me to medical tests, which gave me cancer and left me barren."
Special Agent Chesty Short: "But you don't believe in aliens?"
Scully: "I've seen things that I cannot deny."
Mulder (echoing the Pilot): "It's happening again, Billy?"
Mulder: "More alien abductions, Scully..."
Scully: "I don't know how we could possibly justify the expense..."
Mulder: "We'd probably turn up nothing."
Scully: "Let's go waste some money!"
Mulder: "I've been thinking about it. Looking at you tonight, holding that baby. Knowing everything that's been taken away from you. A chance for motherhood and your health and that baby. I think that... I don't know, maybe they're right."
Sculy: "Who's right?"
Mulder: "The FBI. Maybe what they say is true, though for all the wrong reasons. It's the personal costs that are too high. There so much more you need to do with your life. There's so much more than this. There has to be an end, Scully."
Marita Covarrubias (echoing 1X01: Deep Throat): "They're coming here, aren't they?"
Cigarette-Smoking Man: "They're only coming back."
Mulder (echoing my hopes for the series): "It has to end sometime. That time is now."
Cigarette-Smoking Man's last (?) words: "As you do to Mulder and to me, you do to all of mankind, Alex."
Scully: "I'm having a hard time explaining it or believing it, but... I'm pregnant."