Mulder must again try to track down the alien bounty hunter to save Scully's life but also to find out where the real Samantha Mulder really is.

The episode starts when a navy submarine encounters an unknown vessel beneath the sea and fires on it only to be rocked by a huge shock wave which traps the entire crew underneath the ice.

Meanwhile, Scully realizes that the man inside her room is not Mulder but is the bounty hunter in disguise so she pulls her gun on him only to be tossed aside and taken hostage. Mulder fears for Scully's life and with Samantha, breaks into the motel room only to find that she has gone.

Later, Samantha explains all to Mulder. She says that the Gregors, the clones are setting up a colony on Earth so they can use genetics to merge into the human race. This is why they all worked in the abortion clinics, because they had access to fetal tissue here. But, because the experiment wasn't sanctioned, a secret deal has been set up for a bounty hunter to eliminate the clones.

When Skinner arrives at their door, they realize that the only way to get Scully back is to arrange a trade, Samantha for her. Skinner sets up a sharpshooter while Mulder hands over Samantha. Scully is saved but when Samantha tries to kill the bounty hunter, they both plummet over the edge of the bridge into the river below.

Mulder is distraught that Samantha died so he informs his father who is extremely angry and distressed. He does leave him with something Samantha left for Mulder, the keycard to an abortion clinic where he locates Samantha clones conducting experiments and realizes that the one who died was not really her sister. They explain that his sister is still alive. Soon later, the bounty hunter arrives, knocks out Mulder and kills the remaining clones.

Meeting with Mr.X, Mulder's informant tells Mulder that the pilot's craft was found in the Arctic. Mulder travels up there leaving Scully with a message not telling her where he is going.

Scully is desperate for Skinner to tell her the whereabouts of Mulder so he helps her by starting a fight with Mr. X in Mulder's appartment's lift. He finally gets the answer saying that it was obtained through "unofficial channels".

Meanwhile, Mulder locates the submarine in the Arctic and enters only to discover a surviving soldier who captures Mulder and suddenly morphs into the pilot. Tossing Mulder about, he throws him down to the ice below and starts the submarine up as the conning tower plummets down to the injured body of Mulder lying on the ice.

Back to the present, Scully rushes into a hospital to find Mulder in a tank to heat him up. With her knowledge of the virus which is killing him, she prevents them from heating up his body any further and saves his life. As she lays by his bedside she explains that it was "science that saved Mulder's life" as his eyes blink open to see Scully sitting beside him....