Mulder is dead. But he might not be gone...
Three months after Scully, Doggett, Skinner and Kersh gathered for Mulder's funeral, Doggett is told that he is being transferred from the X Files. If he goes, the X Files will close, as Scully is about to go on maternity leave.
Elsewhere, a fishing trawler catches a body in it's nets. In the county morgue, Dr. Orovetz discovers that the decayed body is still alive. Fingerprints reveal it to be Billy Miles, the teenage abductee who disappeared at the same time as Mulder. Fearing Mulder may still be alive, Skinner gets his body exhumed.
At a hospital, Dr. Lim explains that although Mulder shows signs of life, his body is decomposed. Scully places her head on Mulder's putrefied chest and cries. Later, in Billy Miles's room, she notices that he seems to have two heartbeats.
Kersh tells Skinner to stop the Mulder investigation.
Skinner is walking down a hallway, when the veins in his neck bulge making him stumble. Krycek is triggering the attacks with a Palm Pilot. Krycek tells him he has a vaccine that will save Mulder - he'll give it to Skinner if he ensures Scully doesn't have her baby.
Billy regains consciousness. He stands under a hospital shower, and his decayed flesh sloughs away, revealing a perfectly normal body beneath. He tells Scully and Doggett that aliens are trying to save mankind. Scully has lab reports - Billy has literally become a new person. Skinner tells her that there is a vaccine, but not about Krycek's demand.
Talking to Doggett later, Scully tells him that a virus is keeping the abductees alive long enough to make the transformation like Billy. Doggett tells her that he visited Absalom, who believes that the abductees are being resurrected as aliens in order to take over the world. Perhaps the transformation explains the double heartbeat? Scully asks Doggett to find Skinner and get the vaccine.
Skinner is pulling out Mulder's life support - after a scuffle, he explains that he was trying to kill Mulder because of Krycek's demand about Scully's child. Doggett catches up with Krycek in the hospital car park, where Krycek tries to run him down. After a dramatic scuffle, Krycek smashes the vial of vaccine.
Returning to the hospital, Doggett finds that Mulder has been operated on. Scully explains that the life support equipment was incubating the virus - stabilising him might let them reverse his condition. On regaining consciousness, Mulder asks if anyone missed him. Scully cries.
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