In the beginning of the episode, there is a body wrapped up lying on the floor of an apartment. There is no name mentioned as to the identity, but Scully confirms it.
The rest of the episode is seen as an explained flashback, as Scully is explaining past events to a committee reviewing her work with Mulder on the X-Files. The frozen body of what appears to be an extraterrestrial is found in the St. Elias range of the Canadian mountains. Mulder is contacted about this by Professor Arlinsky, who is working on the expedition, and is sent some ice core samples with DNA in them (presumably alien). Scully has the samples tested and confirms the presence of non-terrestrial DNA in the samples. However, the sampes are stolen, along with the test results by Michael Kristchgau. When Scully confronts him, he flees, but is cornered again and tells Scully that the same people who will kill him if he reveals the truth are the same people who gave Scully her cancer.
Meanwhile, Mulder has ventured to the Canadian mountains where the alien corpse was found, but when he gets to the site he finds that all of the people on the expedition have been shot to death, except for Arlinsky (saved because he was meeting with Mulder), and another man, who says that he has saved the alien corpse from theft by burying it. Together, the three of them recover the alien corpse, and send it back to Washington. There, Mulder and Arlinsky perform an autopsy on the alien, and determine that is in fact extraterrestrial. However, Mulder leaves to meet with Scully, and two men, including the other survivor from the expedition, kill Arlinsky and remove the alien corpse. Mulder meets with Scully and Kritschgau, where Kristchgau explains to Mulder that there are no Aliens, all UFO sightings have been orchestrated by the government, and that Scully was tested on by men, not aliens. These revelations lead Mulder to question all that he has believed in, and be contemplating suicide at the end of the episode, while sitting alone in his apartment.