Scully is in hiding... and in labour.
During an autopsy, metallic vertebrae are found in Billy Miles body. Unobserved, the vertebrae transform into a human figure, and leave the pathology lab.
Reyes and Scully go into hiding in Democrat Hot Springs, where Doggett was born. Leaving Scully, Reyes sees a strange light on the horizon.
Mulder, Skinner and Doggett are investigating apparently impossible photos of Billy Miles leaving the lab. Krycek tells them that Billy is a human replacement - an alien created to aid in Earth's repopulation; a plan which Scully's baby is threatening. Knowle Rohrer, however, tells Doggett that Miles is a prototype 'super soldier'. Doggett is skeptical.
Billy Miles appears at FBI headquarters. Afraid, Skinner runs from his office, narrowly making it to the lift. Krycek, in the lift, makes no effort to help him. Suddenly, the doors are split open by Billy's arm - wounding Skinner. He is taken to hospital.
Doggett tells Mulder that Rohrer claims Billy is a product of a cold war government programme to make super soldiers, and that Scully is part of the programme too. Her pregnancy was triggered by the chip in her neck.
Elsewhere, Reyes and Scully are hiding in an abandoned building. A 4x4 vehicle pulls up, and Reyes pulls her gun, but it is a game warden, offering medical supplies. The warden claims not to have seen the light in the sky. They encounter Billy Miles: Reyes runs, but the game warden shoots him in the chest. The warden tells them she'll have to report the incident, but Scully has started having contractions.
Doggett and Mulder see Rohrer and Krycek enter the FBI building. Rohrer talks to Agent Crane, and Mulder concludes that Rohrer, Crane and Krycek have been fooling them into chasing Billy Miles, when they've known Scully's location all along. Afraid for Scully, Mulder makes Doggett reveal her hiding place. As Mulder goes to his car, Krycek pulls a gun on him. A shot is fired - but it is Skinner, shooting Krycek.
In the abandoned building, the warden is helping Scully - but Reyes notices that she has reptilian vertebrae. She throws boiling water in the warden's face, and grabs her shotgun. Soon after, cars surround the building, and the warden assures Reyes that Scully's baby will be born. Billy Miles picks himself up, and a group surround Scully...
Rohrer and Crane chase Doggett and Skinner - Skinner runs down Crane, who continues attacking. Skinner crashes the car, shaking off Crane who is run over by Rohrer - who also crashes.
Scully gives birth, as Mulder flies to her by helicopter.
Doggett tells Kersh the office is being investigated becasue of the late night meeting he witnessed between Kersh, Crane and Rohrer.
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