Billy Miles is killing... and Scully is in danger.
Scully's mother throws Scully a birthday shower, and hires her a nanny, Lizzy Gill. Scully isn't too happy, but promises to think about hiring a nurse.
Billy Miles confronts Dr Lev in Zeus Genetics. On Saturday morning, Mulder visits Doggett to tell him that Zeus Genetics has burnt down. The debris is searched - Dr. Lev is missing, and Scully's paediatrician Dr. Parenti turns out to be co-founder. Doggett and Mulder confront Parenti about his work. Dental remains in the burnt-out lab are identified as belonging to Dr Lev.
Lizzy Gill, the nurse, has swapped Scully's prescription medication for unidentified pills. She then meets Duffy Haskell...
In Parenti's office, Mulder and Doggett discover Parenti's severed head. Billy Miles is responsible - he attacks Mulder with superhuman strength. Doggett shoots him, but he seems unaffected.
Mulder thinks that Miles is destroying experiments with alien biology. He's concerned for Scully's baby. Lizzy Gill overhears the conversation, and warns Duffy Haskell that their plan is threatened.
Duffy is beheaded by Billy Miles in an industrial warehouse. Skinner tells Doggett it was a human cloning facility.
Mulder phones Scully about her pregnancy, but Scully discovers Lizzy Gill switching her pills as she answers the phone. In hospital, Scully is told her child is fine - the pills were harmless. However, as Mulder and Doggett interrogate Lizzy, she reveals that Scully's child is perfect - without human frailties. Mulder visits Scully and tells her to leave, as she is in danger.
Billy Miles is in Dr Parenti's office, and wants to give himself up. When Doggett and Crane investigate, he's gone - it was a diversion. Mulder is hurrying Scully to her car as Billy Miles appears - but he is run down by Alex Krycek.
Krycek drives Mulder and Scully to FBI HQ, explaining that 'human replacements' such a Billy are trying to stop humanity surviving the coming alien invasion. These replacements are scared of Scully's baby, as it is more than human. Krycek wanted to destroy the child to stop the aliens learning of a higher power - God.
Billy Miles infiltrates the FBI building, and Mulder asks Krycek to protect Scully. Miles follows Skinner on to the roof, where Mulder pushes him off the roof into a garbage truck, where he is crushed. Reyes drives off with Scully, observed by Agent Crane - who has spiked vertebra at the back of his neck...
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