After Agent Mulder goes beyond his jurisdiction to shine light on a possible X-file, Doggett is assigned to investigate the mysterious disappearance of two men aboard an oil rig. Once he arrives, he finds Mulder has taken it upon himself to start his own investigation. Mulder soon becomes convinced that the rig is drilling the black oil. Doggett and Mulder must attempt to stop the spread of the alien virus while avoiding the infected crew.

Mulder and Doggett join forces to investigate the arson attack on a genetics lab where one of the doctors suspected of experimenting with alien impregnation is killed. They encounter Billy Miles, who has been changed into an alien replicant after his recent abduction and is attempting to erase evidence of the tests; part of the Syndicate's conspiracy with an alien race. When a woman helping Scully out at home is found to be a part of the conspiracy, the agents, along with Monica Reyes and Alex Krycek, know they must protect Scully and her baby from Billy Miles and get her out of the city.