Three months later, Doggett is called into Kersh’s office where Skinner is waiting. Doggett has been recommended for advancement and transfer off the X-files, but Doggett asks for more time to consider such a move. He goes back down to the X-files office where a noticeably pregnant Scully is poring over case files. She tells him to accept the transfer, noting that if he doesn’t get out now he may never get out at all. Although he has found Mulder, Doggett feels he still has more questions about the case and is reluctant to leave. Meanwhile, a fishing boat in Wilmington, NC catches sight of a body in the water. The body has scarring that is reminiscent of the alien tests. When a coroner goes to examine the body, he is astonished to see the dead man’s lips move. Skinner awakes Doggett to tell him that the body found in the water is Billy Miles, who was presumed dead for months and is now alive. Doggett advises Skinner not to relay this information to Scully. They go to the graveyard in Raleigh to unearth Mulder’s body.
Scully runs into the US Naval Hospital in Bethesda, MD distraught and full of wide-eyed emotion, demanding to see Mulder. “Tell me it’s true,” she pleads with Skinner. Although he has thin life signs and is clinically alive, Mulder’s body is in a full state of decomposition. Scully is teary as she approaches Mulder, and she rests her head on his chest as it rises and falls with each breath. She then goes into the hospital room of Billy Miles, whose body begins to convulse. The heart monitor briefly shows two heartbeats, and Scully notifies the nurse that the equipment may be malfunctioning.
Kersh summons Doggett to his office and orders him to drop the Mulder investigation. Doggett is wary of his superior’s intentions. Walking down the FBI hallway, Skinner almost loses consciousness when the familiar black veins suddenly appear on his face and neck. He opens the elevator doors to find Krycek with the handheld device that controls the nanotechnology. “What do you want from me?” Skinner asks. Krycek says that he has the vaccine developed by Bill Mulder that will save Mulder’s life. “You found him and you don’t even know what you’ve got,” Krycek says elusively before leaving Skinner empty-handed. Meanwhile, Billy Miles wakes up in his hospital bed. He pulls out the life support tubing and, still bloated, walks into the shower. As the water covers him, his hardened skin peels off leaving a perfectly fine human body underneath. Down the hall, Scully sits with Mulder while Doggett conveys his concern about reopening this case. She wants to know the truth about what caused this to Mulder. Suddenly, a nurse interrupts them. A healthy Billy Miles is walking naked in the corridor, looking like a recently hatched chick.
Doggett goes to see Absalom. “You ask for my help but you refuse to believe in me,” the alien healer says to the skeptical agent. Back at the hospital, Skinner looks in on Mulder but finds Krycek lurking in the corner. When Skinner asks for the vaccine, Krycek tells him he only has to make sure that Scully doesn’t come to term. Skinner refuses to sacrifice Scully’s baby, but considers the deal. Doggett passes Krycek in the hospital hallway, but doesn’t know who the man is. He stops to talk to Scully, who believes that Mulder was infected with a virus that transforms the body into an alien. Doggett notes that Absalom had said the same thing. They now believe that Billy Miles is somehow alien, and she asks Skinner to do whatever it takes to retrieve a vaccine. When Doggett returns to Mulder’s room, the door is locked. He finds Skinner has pulled out all the life support tubes, intending to kill Mulder. An enraged Doggett attacks Skinner, who admits that he couldn’t trust Krycek’s claims of a virus if it meant jeopardizing Scully. With gun drawn, Doggett takes off after Krycek in the parking garage. He latches on to Krycek’s moving car, grabbing for Krycek at the wheel, but lets go before the car narrowly escapes. Krycek puts the car in reverse and comes back. He holds up a vial and asks Doggett if he is looking for the vaccine to save Mulder. Doggett takes one step forward and Krycek drops the vial, splattering the brown-colored liquid on the ground.
Doggett goes back upstairs and finds that Mulder was taken into the operating room. Dressed in scrubs and watching the procedure, Scully comes out to tell Doggett that they had been incubating the virus by keeping Mulder on life support. Skinner actually saved him when he pulled off the machines. She has faith that a course of anti-virals will work. Doggett is once again called to Kersh’s office where he gets sent back to work on the X-files.
In the recovery room, Scully takes Mulder’s hand and he flinches. His eyes flutter open. “Who are you?” he jokes. Scully laughs for the first time in a while and leans across his body, holding him. “Anybody miss me?” he says. Doggett sees this reunion through the window, and Scully looks up at him, not knowing what to say. Doggett relieves her of the trouble and walks away, alone.
Original Air Date: 04/01/01
Written by Chris Carter & Frank Spotnitz
Directed by Tony Wharmby
DAVID DUCHOVNY as Special Agent Fox Mulder
GILLIAN ANDERSON as Special Agent Dana Scully
ROBERT PATRICK as Special Agent John Doggett
Mitch Pileggi as A.D. Walter Skinner
Nicholas Lea as Krycek
James Pickens, Jr. as Deputy Director Kersh
Tom Braidwood as Frohike
Dean Haglund as Langly
Bruce Harwood as Byers
Judson Scott as Absalom
Zachary Ansley as Billy Miles
Sheila Larken as Mrs. Scully
Gibby Brand as Arthur Gaffin
Larry Dorf as Pathology Assistant
Richard McGonagle as Dr. Orovetz
Arlene Pileggi as Skinner’s Assistant
Nelson Mashita as Dr. Lim
David Doty as Minister
Mary Wickliffe as Nurse
Larry Rippenkroeger as Deckhand