Mulder searches for the real truth about alien life but his pursuit means that any one of them could be in grave danger. It is a season finale that will shock us all.

Scully enters Mulder's appartment where a body is covered up in sheets surrounded by Detectives and Forensic scientists. Detective Rempulski uncovers the sheets and Scully positively identifies the body finding it hard not to lose control. This leads Scully to a meeting with Chief Scott Blevins where she explains the circumstances of how she was introduced into the X-Files division to debunk Agent Mulder's work.

The story now unfolds in flashback. A pair of anthropologists, Arlinsky and Babock make their way to the base of a mountain covered in snow to a camp. The pair then, accompanied with a guide, make their journey inside a cave where they discover a perfectly preserved body of a gray alien frozen inside the ice.

At Mrs Scully's house, some guests gather round for a dinner party including Scully's brother, Bill Scully Jr. and a Catholic priest, Father McCue who was obviously sent to join them by Margaret so that Scully could discuss her faith with him at a time when her life is threatened by cancer. Afterwards, the priest and Scully begin to discuss how she has drifted away from the church when she receives a phone call. It turns out to be Mulder who has just been informed about something unearthly discovered in Canada. He arranges for him, Scully and Arlinksy to meet at the Smithsonian. Arlinksy wants the agents to come along as he wants them to verify the aliens remains claiming that they are over 200 years old.

Mulder and Arlinsky go up to a deserted base camp where an unknown assassin has killed off all the Summiteers with a shotgun unknown to Mulder and Arlinsky. They soon discover, after reaching the summit of the mountain, the bodies of Babcock and a foreman. The pair cannot find the alien in the cave as it seems to have disappeared but later Babcock who is alive but badly injured, tells them that he buried it beneath his tent away from harm.

While Mulder is away, Scully and a scientist named Vitagliano push forward with their own investigation of the ice core samples from the cave. Later at night, Scully returns to the lab alone only to be assaulted by an unknown person and tossed down a flight of stairs. Agent Hedin manages to match the fingerprints found on the bannister of the stairs to a man who works for the Pentagon, Michael Kritschgau so Scully confronts him and arrests him on site. The man warns Scully that if he goes to jail then the people who gave Scully cancer will kill him.

Meanwhile, Mulder transports the alien body with Arlinsky to an abandoned warehouse where they can perform and autopsy. Scully rings Mulder up at the warehouse and arranges a meeting with Mulder so that Kritschgau can tell his whole story to him. Shortly after, the same assassin up at the mountain murders Arlinsky and Babcock. Kritschgau tells his story to Mulder saying that the government has created a hoax in order to divert Mulder away from the truth. He adds that the alien they found was in fact a fake and man-made and that Mulder was meant to see it so that he could believe it. Mulder thinks that what the man is telling him is all lies so he storms off but soon discovers that the alien body is gone and the dead bodies of Babcock and Arlinsky. Later, Scully tells Mulder that the men responsible for the hoax gave her cancer only to make him believe the hoaxes they were performing which shocks Mulder.

Back to the present day, Scully tells the FBI officials that she received a phone call from the police department asking her to identify a body. Almost breaking down in tears she tells them that Mulder died of a self-inflicted gunshot wound to the head.......