Abductees start being returned in a very bad shape. Jeremiah Smith, with the help of UFO cult leader Absalom, recovers them and heals them. Agent Monica Reyes is brought in to help in the investigation. As Mulder is found, Jeremiah is abducted. Mulder is buried, much to Scully's grief. Three months later, Billy Miles is found, and he's still alive. Mulder is exhumed and is still alive as well. The returned abductees like Billy go under a transformation led by a variant of the Black Oil virus, from human into an alien facsimile with a human body and an alien conscience. For some reason, Krycek wants Scully's baby dead. Thanks to extraordinary coincidences, Mulder miraculously recovers.
The much-hyped return of Mulder finally happens, and the writers aren't kind to him: scarred, tortured, declared dead, buried, exhumed. But Mulder is tough! A month separates the airing of This Is Not Happening from that of DeadAlive, both to allow the despair of the situation to sink in the viewers' mind, but also to launch the ill-fated spin-off series "The Lone Gunmen". Duchovny's involvement is spread very thin to satisfy rabid fans that only demand for Mulder & Scully: the marketing centres around his character heavily for every single appreance, as short as it may be (8X01: Within, 8X02: Without, 8X08: Per Manum, 8X10: The Gift, these two episodes). And as soon as he's back he's the first to be credited in the opening titles: I wouldn't want to be Robert Patrick! Carter & Spotnitz, walking on a fine line of improvisation once again, made the choice to focus the series around Mulder's persona -- perhaps preventing the show from moving on to new ground.
Abductees left for dead
Months after the great sweep of 7X22: Requiem and 8X01: Within / 8X02: Without, alien activity stopped. Then it started again, this time with abductees being returned in a rather bad shape, close to death ("After Oregon there wasn't a whole lot, but then all of a sudden in Montana..."). The alien Colonists seem to dump the bodies of the abductees, apparently careless of their fate. They bear the marks of heavy and painful experimentation on them: "Inside her cheeks there's tissue damage in a linear pattern. Her chest was cut into and organ tissue in her abdomen's scooped away. In the X-rays I see damage to the soft palate." "cuts and abrasions from ligature or binding devices accompanied by distal and proximal bruising radiating in a symmetrical pattern around the ankles, the wrists and the face." These are consistent with the flashes we see of Mulder being tested on, so these flashes are not just nightmares Scully had. Scully dreaming this is probably due to this intense spiritual bond they have created between them, further evidenced in her vision of Mulder's spirit in her motel room right before Mulder's body is discovered -- much like the visions of 1X12: Beyond the Sea or 7X11: Closure. Speaking of Closure, Scully has a nice discussion with Skinner about starlight, remembering what she and Mulder had talked about concerning souls and the Walk-ins. The abductees have no implants in them, the first indication that these are of a different kind. We see Richie Szalay again (after Requiem); like Scully was hunting for Mulder, he's been hunting for his abductee friend Gary.
Jeremiah Smith and Absalom
Absalom is a "religious zealot" with a sinful past ("credit card fraud" among other things it seems) who became "the nominal leader of a doomsday cult who believed aliens would take over the world at the millennium". After the turn of the millennium he started what looks like a UFO cult in a ranch in Montana. His crazy prophet aspect doesn't lend him much credibility (Absalom: "You're here to receive the word and yet you can't bring yourself to say my name. Say it!"), yet there is some truth in his sayings. Especially since he partners with somebody we thought was dead: Jeremiah Smith from 3X24: Talitha Cumi / 4X01: Herrenvolk, the alien/human hybrid with religious overtones who rebelled against the Project and used his powers to heal to 'spread the word'. There were many Jeremiah Smith clones, all apparently rebellious against the Syndicate and the Colonists; the one we knew obviously died (the Alien Bounty Hunter had hunted him throughout the episode, it's unlikely he escaped at the last moment), the one we meet here is the last surviving one ("I'm the only one"). Jeremiah used his healing powers to help the injured abductees, to save them from their alien sloughing destiny. Jeremiah somehow knew where the abductees would be returned (thanks to his mind-reading abilities?); he and Absalom were there each time an abductee was returned. When Teresa Hoese (from Requiem) was taken to the hospital, where she would certainly have turned alien, Jeremiah shapeshifted to the hospital's doctor to transfer her back to Absalom's camp. Scully recognized the shapeshifting Jeremiah thanks to his Nike shoes.
But this isn't over yet. Three months later, Billy Miles' body is found at sea, with an extreme "intumescence" (the swelling). The entire body showed all the signs of a dead body ("the body had rigored. For all intents and purposes, he was dead"), yet against all odds he is alive: "heart beat, rate of metabolism, it slowed to imperceptibility".
Billy is put on life support. Scully witnessed a seizure and what looks like "two heartbeats" on the monitor, then back to 'normal': Scully had just seen Billy Miles dying and the alien conscience taking over. Soon after, 'Billy' wakes up and sheds his swelled skin; under it, he looks pristine. This is very akin to the evolution of the Black Oil alien, the 'creature' alien shedding its skin to become a normal grey alien (6X01: The Beginning). The new Billy is too normal to be true: "there isn't a piece of medical data on him that isn't 100% normal. [...] there should be blood fluid, electrolyte imbalances, loss of brain function. But as it is, it's like he shed his skin and literally became a new person. And I don't mean the same person." Billy, like all the other abductees all over the world who were not cured by Jeremiah, has been replaced by a being with an alien conscience in a human body -- an alien facsimile (8X18: Three Words) or Supersoldier (8X21: Existence). He looks disoriented and tells lies to Scully: "But now I understand. They [the aliens] are here to save us." This is the stories that the aliens were telling Cassandra Spender (5X13: Patient X), luring her away from the truth. After this, Billy just went on his normal alien business, inexplicably left unmonitored by Scully & Doggett.
Krycek offers a vaccine as the cure to Mulder's problems. Evidently this is the same vaccine we know of against the Black Oil (same reddish colour; 5X14: The Red and the Black, Fight the Future). Krycek: "Mulder knows of it. His father developed it to fight the alien virus." (This is a bit of a stretch, as Bill Mulder only started the project in the USA, he never saw it bear fruit.) The virus at work here, "seems to keep the body just alive enough to take it through a transformation" from human to alien. We haven't seen the Black Oil act this way before; this must be a slightly modified version of the Black Oil, designed by the Colonists themselves and personalized to each abductee (hence the extensive tests onboard the UFO), that incorporates human physiology and alien development (skin shedding) and consicence. After the transformation, no traces of the virus are to be found ("100% normal"): the Black Oil virus resides within the genome of the transformed being, fully fused with its human parts in an indistinguishable whole.
Mulder's miraculous recovery
Something that remains unexplained is why Mulder was not autopsied (like Gary when he was found, and like Billy was about to be); this would certainly have been the end of him... but it still is the normal procedure! And as another miracle, Mulder is not healed by Jeremiah and does not receive the vaccine, yet he recovers! "By keeping him on life support we were incubating the virus, we were hastening it along." Indeed Billy's transformation was accelerated once he was pulled out the sea an put on life support. Helping the (human) body metabolism also helped the virus's. "When Skinner pulled Mulder off of the machines, his temperature dropped rapidly without affecting his vital signs." Under a lower temperature, it is known that the alien virus, under any form, works less effectively (2X17: End Game, Fight the Future). But in this state, the virus should still have completed its task, otherwise the whole alien operation would have been for nothing: the abductees that were not found and went through their transformation must by far outweigh those that were found. Surprisingly, Scully solves the action of the virus by plain conventional treatment: "If we can stabilize him and his temperature we can give him courses of antivirals". If the Black Oil virus could be fought with conventional medicine, then why all the fuss with the search for immunity and a vaccine? Evidently this version of the virus is quite different, somehow weak, as the transformation it triggers lasts for months and it goes on a much bigger depth than a 'normal' infection with a gestation (which barely lasts a few hours, 6X01: The Beginning). Also, Mulder's great history definitely played a vital role in further weakening the virus: his exposure to the Black Oil and him being administered the vaccine (4X09: Tunguska) might have left him some antibodies; also, some immunizing Black Oil might have remained after his operation (7X04: Amor Fati). Still, his recovery sound very miraculous -- even in the world of extreme possibilites of the X-Files...
- Gary Edward Cory: dead & autopsied
- Teresa Hoese: healed
- Billy Miles: successfully transformed into a Supersoldier
- Fox Mulder: not autopsied & saved
Krycek's back with another dubious agenda. He uses the means of pressure he has on Skinner, the nanobots in his bloodstream (6X10: S.R.819), to get what he wants. He asks for Skinner to kill Scully's baby: "Make sure Scully doesn't come to term". He doesn't explain why "she can't have that baby", but obviously he has learned of the alien prophecy that her son will be the leader of the alien Colonists (9X11: Providence), probably by studying the Ship's artifacts he inherited after the Cigarette-Smoking Man left the scene (7X04: Amore Fati, 7X22: Requiem). And, as a good man that wants to resist the Colonists, he wants the prophecy disproven -- by cynically condemning the life of Scully's baby. Unfortunately for him (and for everyone?), Skinner doesn't comply. It's touching that Skinner chose the life of Scully's baby over that of Mulder's: indeed Scully's baby is enough of a miracle and gave meaning to her life, whereas everybody has been mourning Mulder for the last three months anyway. In a great moment of irony, Skinner's attempt to kill Mulder (taking him off life support) is what saves him. Mulder and Scully's baby survive and Krycek, now certain that the X-Files gang wouldn't comply, viciously destroys the vaccine before Doggett's eyes. Nobody may see it yet, but for the time being he is still acting for the benefit of mankind. He will be back in 8X20: Essence with another surprising strategy.
Reyes & Doggett
After Mulder is found, Doggett gets an offer for a promotion. This temptation is the definite stratagem to close the X-Files ("In six weeks, you go on maternity leave. Kersh transfers me out, guess what? He gets to lock that door over there for good."). Scully's experience warns him: "Get out while you can, Agent Doggett. Or you may never get out at all." But Doggett has become too involved. His chivalric protection of Scully and his determination to have everything explained makes him decide to stay; he misses his chance out. Kersh: "It's going to be awfully crowded down in that X-Files office." Scully's belly finally shows.
This Is Not Happening
Scully: "What is it you specialize in again? Ritualistic crime?"
Reyes: "Right. Satanic ritual abuse. Or, I should say claims of it: we never found any hard evidence."
Scully: "We should talk sometime."
Scully (discovering all hope is lost): "No... No!... This is not happening! Nooo!"
Scully (in Mulder's funeral): "He was the last. His father and mother, his sister, all gone. I think the real tragedy is that for all of his pain and searching, the truth that he worked so hard to find was never truly revealed to him. I can't truly believe that I'm really standing here!"
Skinner: "I know. And I don't truly believe that...Mulder's the last."
Scully: "Get out while you can, Agent Doggett. Or you may never get out at all."
Scully: "Agent Doggett... However I felt about you when we first met, you changed my opinion with the quality of your character and of your work. Now, I am thankful to know you and I am thankful for your concern. But no matter what Mulder's chances are, the choice not to open up that grave was wrong. And not because of me personally, but as my partner on the X-Files. Now, the truth may hurt but it's all that matters."
Krycek: "We all have a life in our hands. I have yours. You have Mulder's. And Scully has her unborn child. It's who's willing to sacrifice."
Kersh: "It's going to be awfully crowded down in that X-Files office."
Scully: "Do you have any idea what you've been through?"
Mulder: "Only what I see in your face... Anybody miss me?"