Mulder and Scully must race to track down an alien bounty hunter before he disposes with the last remaining truth that could separate Mulder and his sister.

At the start we witness Mulder being rushed to hospital by helicopter suffering from extreme hypothermia. In a voice-over he explains that he has found extra-terrestrial life and that they have begun to "colonize" among us.

In a flashback, we go back two weeks to the Beaufort Sea where a ship has discovered and rescued a Russian pilot after crash-landing. Meanwhile, a doctor at an abortion clinic watches the news about the incident when he rushes out of the room quickly only to be confronted by the same pilot who stabs him with a strange weapon. He leaves the doctor on the floor oozing green fluid.

Back at FBI Headquarters, Mulder has received three obituaries detailing the deaths of the doctors who all seem to share exactly the same likeness. Mulder, after some investigation, realizes that there may still be some of these doctors being hunted down and so calls up a fellow agent in Syracuse to keep a close watch on another of the doctors. When he turns up, the pilot is there but has already killed the doctor who also oozes green fluid. The agent shoots him but suddenly covers his eyes at the strange radiation which emits from the wound on the pilot. The shot doesn't harm him.

Mulder and Scully arrive and encounter their fellow agent who tells them that the doctor never turned up. When they leave, the agent suddenly morphs into the pilot and leaves the agent's body in the trunk of his car, dead.

Skinner later informs Mulder that the agent in Syracuse was found dead which confuses him.

Later, as Mulder is outside Scully's appartment, he meets a CIA agent named Ambrose Chapel who explains that the doctors are actually Soviet clones codenamed "Gregors" and that they are being disposed of by an alien bounty hunter. With Chapel, they locate another doctor who quickly runs off flying through a window, gets up and runs off. Mulder and Chapel follow but Mulder is knocked down by a car. Chapel morphs into the pilot when he finds the doctor and kills him with the same weapon leaving him in a pool of some more green fluid.

Later, Mulder receives a call from his father who tells him to quickly come home where he finds that his sister, Samantha has returned after 22 years away.

She explains to Mulder that the Gregors are her adoptive parents who are actually aliens being killed by the bounty hunter who can disguise himself as anyone. Mulder realizes that Scully may be in immediate danger.

Meanwhile, Scully finds the remaining four Gregors and places them in protective custody. Even this is not enough though, as the bounty hunter soon enters disguised as an agent and kills all of them.

Scully hires a motel room for the night but doesn't hear the phone call which Mulder makes. Soon after, Mulder enters saying that he has been trying to contact her. Suddenly the phone goes. She finds that Mulder is on the line as she turns to face the man in her room.........