S2E17 · End Game

USS Allegiance, an American nuclear submarine, is patrolling the Beaufort Sea off the coast of Alaska when it comes across a craft below the ice that is emitting a radio signal. Allegiance is ordered to fire upon the craft by Pacific Command. However, the craft manages to disable the sub using a high-pitched frequency, stranding it below the ice.

Continuing from the cliffhanger ending of " Colony ", Dana Scully (Gillian Anderson) is beaten and kidnapped by "Mulder", who is really the Alien Bounty Hunter in disguise. When the real Mulder (David Duchovny) finds the wrecked hotel room, his sister Samantha explains that the Bounty Hunter will set up a hostage exchange to swap Scully for her. She further explains that the Bounty Hunter can only be killed by piercing the base of his neck and that his alien blood is deadly to humans. Finally, Samantha reveals that the clones are the progeny of two original aliens and worked at abortion clinics to gain access to fetal tissue. Their objective was to set up an extraterrestrial colony on Earth, an effort that has gone as far back as the 1940s. Because the clones' experiments were considered to have tainted their alien race, the Bounty Hunter was sent to kill them.

Walter Skinner meets Mulder and Samantha at Mulder's apartment, telling them that the remaining clones are missing. Mulder receives a call from Scully, who tells him that the Bounty Hunter seeks an exchange for Samantha. Mulder and Samantha are sent to a bridge near Bethesda while Skinner hides nearby with a sharpshooter. After the exchange takes place, Samantha attacks the Bounty Hunter. During the struggle, the sharpshooter fires upon the Bounty Hunter, and both he and Samantha fall into a river. An anguished Mulder tearfully apologizes to his father, Bill, for losing her again.

Bill leaves Mulder a note from Samantha, which provides him with the address of a Maryland clinic where they can meet if separated. Mulder hopes that she is alive, but soon gets a call from Scully reporting that Samantha's body has been found. After Scully ends the call, she discovers Samantha's body dissolving into a green liquid.

Meanwhile, inside the clinic, Mulder finds multiple clones of Samantha working on fetuses in labs similar to that of the clones. They reveal that they manipulated Mulder by sending one of their own to pose as "Samantha" in an effort to have him protect her original clone. They claim to know the real Samantha's location. Mulder, realizing he has been duped, initially refuses to help and starts to leave, but is knocked unconscious by the Bounty Hunter, who proceeds to kill the Samantha clones and burn down the clinic. When no trace of the clones is found, Mulder meets with X at the Kennedy Center, demanding to know the Bounty Hunter's location.

X says that the Bounty Hunter's craft below the Beaufort Sea has been found, and that a naval fleet has been sent to destroy it. Mulder heads there and e-mails Scully to tell her not to follow him.

Scully goes to Skinner for help, but he initially refuses. She summons X to Mulder's apartment, but he turns her down. On his way out, X is confronted by Skinner in an elevator. After the two men engage in a vicious physical altercation, X divulges Mulder's whereabouts. Meanwhile, Mulder finds the stranded Allegiance, with its sail broken through a patch of shallow Arctic ice. Inside, he finds what seems to be the sub's only surviving crewman, whom Mulder realizes is the disguised Bounty Hunter. The two struggle, during which Mulder becomes exposed to the Bounty Hunter's toxic blood.

The Bounty Hunter claims that Samantha is still alive before dumping Mulder off the sail and submerging Allegiance; a weak Mulder is nearly cut in half with the sub's diving plane in the process. He is discovered and rushed to the field hospital seen at the beginning of "Colony", where Scully—having learned that the alien blood contains a retrovirus that dies in cold temperatures—convinces the doctors to take him out of the bath that would warm up his body.

As Mulder's condition stabilizes, Scully writes a field report crediting science with detecting the retrovirus and saving Mulder. She contends that the retrovirus is of a mysterious origin, and reports that neither the Bounty Hunter nor Allegiance have been found. When Mulder regains consciousness, he tells Scully that his experiences did not give him the answers he had been searching for, but that they have given him renewed "faith to keep looking".