Mulder's funeral is held at the family grave in North Carolina. Three months later, Kersh tells Doggett that he's recommending him for advancement due to his efforts in finding Mulder. Doggett suspects that Kersh wants to shut down the X-Files once he's transferred and Scully goes on maternity leave, but Scully urges him to take the promotion anyway. The bloated body of Billy Miles is found off the coast of North Carolina, and it turns out that he's alive. Thinking the same might be true for Mulder, Skinner has his coffin exhumed. It turns out that Mulder is clinically alive, despite the fact that some of his systems are decomposing; Kersh warns Doggett to leave the matter alone so the FBI doesn't look bad.
Miles sheds his dying skin, regaining his normal appearance, and says the aliens are actually there to save mankind. Scully suspects that he may have transformed into something else. Doggett visits Abasalom in a West Virginia prison to try to get some insight on the healing process, but that remains unexplored for the rest of the episode. Krycek, who has returned with his nanobot blackmail device, makes Skinner an offer: he'll give up the anti-alien vaccine needed to keep Mulder alive, providing Scully's baby doesn't live. Skinner refuses the deal, though Scully tells Doggett that she had asked Skinner to get the vaccine; she thinks Miles was infected with a virus that started the transformation, and believes the vaccine can stop the same thing from happening to Mulder.
Doggett finds Skinner trying to pull the plug on Mulder; he tells Doggett he can't trust Krycek and certainly can't betray Scully. Doggett chases Kryeck, but he escapes and taunts Doggett by destroying the vaccine. Meanwhile, Skinner's action has shown that the virus is being incubated by life support, and Scully says Mulder might be able to recover on antivirals alone. Kersh lets Doggett know that his promotion is no longer on the table. Much to Scully's joy, Mulder wakes up unaffected by the virus.
Episode Body Count
No new deaths. However...
Agent Fox Mulder: of course they're not going to kill Mulder! He is found to be not quite dead yet three months after his funeral.
And so this episode ties for Least Deadliest of Show with Dreamland II.
Cumulative Body Count (176/202 episodes, 1/2 movies)
Humans: 2,020Creatures: 126
Grand Total: 2,210