EXISTENCE

A metal box containing the remains of Billy Miles is brought to a coroner. The coroner examines it and notices what appears to be a metal vertebra. After he leaves the room, the metal vertebra begins to spin, growing into what looks like the beginnings of a metallic spine. Meanwhile, Dana Scully (Gillian Anderson) and Monica Reyes arrive at the abandoned town where Special Agent John Doggett (Robert Patrick) was born.

Alex Krycek (Nicholas Lea) is seated in a chair in Assistant Director Walter Skinner's office, where he is shown a video from the morgue. Skinner tells him that Miles is somehow alive and still out to get Scully and her unborn child. Suddenly, Agent Gene Crane comes to Doggett and tells him that there is a person—Knowle Rohrer—who wants to see him about issues concerning Miles and Scully. This leaves Fox Mulder and Skinner to interrogate Krycek. Rohrer tells Doggett that Miles is part of a secret military project to create "super soldiers" and that Scully had a chip put in the back of her neck during her abduction to make her pregnant with the first organic version of a super soldier.

In Skinner's office, Krycek tries to leave. Skinner goes after him, then turns around and sees Miles approaching behind him. Skinner just manages to escape with Krycek, but Miles' hand breaks through the elevator door, injuring Skinner and knocking him unconscious. At the hospital, Mulder distrusts what Doggett has been told by Knowle Rohrer, so the two set out to find out how trustworthy he really is. Meanwhile, as Reyes and Scully are hiding out, Reyes sees someone running off and follows them. A car pulls up and she meets a trooper who agrees to help with the birth. As Mulder and Doggett pull into the garage, they find Krycek pulling up in another car, with a passenger who happens to be Rohrer. Mulder believes that Rohrer and Krycek are colluding together but don't understand why. Doggett covertly pursues Rohrer and learns that he has an accomplice: Agent Crane.

Mulder's own problems arise when his cell phone rings and Krycek disappears from his car. Mulder, after learning what Doggett has witnessed, believes that Crane gave Krycek access to the FBI. Suddenly, Krycek smashes through the car window with his prosthetic hand and crushes Mulder's phone. Krycek threatens Mulder with a gun, but a bullet administered by Skinner pierces his arm. Krycek tries to pick his gun up again, but Skinner shoots his hand, rendering it useless. Krycek pushes his gun over and tells Skinner to shoot Mulder, claiming Mulder's life will grant him a thousand lives. Instead, Skinner shoots Krycek in the head. Doggett attempts to apprehend Rohrer and Crane but ends up being chased by the two. The pursuit ends violently with Crane being run over and Rohrer crashing his car into the garage wall, going up in flames. Both men are presumed dead.

Scully goes into labour and Reyes helps her deliver an apparently normal baby, with alien Super Soldiers surrounding them and witnessing the birth in a cold stare. Without explanation, the aliens leave the area as Mulder arrives. While Doggett and Reyes report to FBI Headquarters, Doggett initiates an investigation into Deputy Director Alvin Kersh after previously witnessing a late night meeting between him, Rohrer and Crane (and their consequent disappearance). Mulder takes Scully and their baby back to her apartment. After marveling over the baby and discussing recent events, the two share a long, passionate kiss

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