S8E21 · 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.

In Assistant Director Walter Skinner 's office, a surveillance video shows Billy Miles leaving the morgue alive and well. Questioned by Skinner and Agents Mulder and Doggett, Alex Krycek (Nicholas Lea) reveals that Miles is a "new type of alien replacement agent" and there are others like him. Doggett is called out of the office on behalf of his source Knowle Rohrer, who claims 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.

Suddenly, Miles appears at the FBI headquarters. Sensing this, Krycek tries to escape with Skinner in pursuit, but as they manage to escape in an elevator, Miles' hand breaks through the elevator door, injuring Skinner and knocking him unconscious. At the hospital, Doggett relates Rohrer's claims to Mulder, who rejects the story, and the two agents set out to find out how trustworthy Rohrer really is. As they observe the FBI garage, they see Krycek and Rohrer arriving in a car. Doggett covertly pursues Rohrer and sees him meet with FBI Agent Crane.

After learning of this, Mulder believes that Crane gave Krycek access to the FBI. Suddenly, Krycek smashes through the car window and crushes Mulder's phone. Krycek threatens Mulder with a gun, but is disarmed and eventually shot dead by Skinner. Doggett confronts 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 but later disappear.

Meanwhile, Dana Scully (Gillian Anderson) and Monica Reyes have arrived in Georgia at the abandoned town to hide Scully and her unborn child. They are detected by a female trooper, who agrees to bring them supplies for the birth. At night, Miles attacks the hideout but is shot by the trooper. Scully goes into labor, while a revived Miles and other alien Super Soldiers surround the house. The trooper, revealed to be another Super Soldier, exclaims: "This baby will be born!" Monica Reyes helps Scully deliver an apparently normal baby, with the Super Soldiers witnessing the birth in a cold stare. Without explanation, the aliens leave the area as Mulder arrives.

At FBI Headquarters, Doggett and Reyes report to an enraged Deputy Director Alvin Kersh, who objects to Doggett co-opting Reyes to the X-Files without his permission. Doggett retorts by informing Kersh that he is himself under investigation after a late night meeting between him, Rohrer and Crane. Mulder visits Scully and her baby, William, at her apartment. After marveling over the baby and discussing recent events, the two share a long, passionate kiss.