Scully enters Mulder's apartment, where a group of detectives and forensic technicians are waiting. Detective Rempulski introduces himself, then pulls back a sheet draped over a body lying on the floor. Scully positively identifies the victim. Later, Scully appears before a group of FBI officials led by Section Chief Scott Blevins. During the meeting, Scully recounts how, four years earlier, Blevins assigned her to a project known as The X-Files. She states that the purpose of the current meeting is to report on the illegitimacy of Mulder's work.

     In flashback, a pair of anthropologists, Arlinsky and Babcock, are flown by helicopter to a snowbound camp at the base of a mountain. Accompanied by a guide, the pair make their way up the steep terrain. Upon reaching the summit, the men enter a cave where the body of a gray alien is perfectly preserved in ice.

     A group of guests gather at Mrs. Scully's house for a dinner party. Amongst the attendees are Dana's brother, Bill Scully, Jr., and a Catholic Priest, Father McCue. Scully realize McCue was invited by her mother for the purpose of discussing her faith at a time when Scully's health is at great risk due to her cancer. After dinner, Father McCue and Scully briefly talk about her drifting from the church before their discussion is interrupted by a phone call from Mulder. He has received information about a something that was discovered in Canada.

     Mulder arranges for Scully to meet he and Arlinsky at the Smithsonian. Arlinsky claims that, based upon ice core samples taken from the scene, the alien body is some two hundred years old. He asks for the agents' assistance in verifying the alien remains. Mulder and Arlinsky fly to the base camp, which is eerily deserted. Unbeknownst to them, a mysterious assassin armed with a shotgun pistol has murdered the Summiteers. Upon reaching the summit, the men discover the bodies of Babcock and a foreman. Inside the cave is a rectangular hole where the alien body had been entombed. Later, Babcock, injured but alive, tells the pair that he buried the alien body beneath his tent.

     Meanwhile, Scully and lab scientist Vitagliano examine ice core samples taken from the cave. Later that night, Scully returns to the Bio Lab, where she is assaulted and thrown down a flight of stairs by an unidentified attacker. Agent Hedin matches fingerprints found on the stairwell to a Michael Kritschgau, who works for the Pentagon's research division. After viewing a personnel file, Scully positively identifies Kritschgau as her attacker. Later, she confronts Kritschgau inside a parking garage and places him under arrest. But Kritschgau warns that if he is taken to jail, the same people who gave Scully cancer will kill him.

     Mulder and Arlinsky transport the alien body to a warehouse where an autopsy can be performed. Scully contacts her partner at the warehouse and arranges a meeting so he can hear Kritschgau's story firsthand. Soon afterward, the assassin, Ostelhoff, shoots and kills Arlinsky and Babcock at the warehouse. Meanwhile, Kritschgau, who claims to have run the Department of Defense's agitprop arm, tells the agents that the government has been orchestrating an elaborate hoax to divert attention away from itself. The alien corpse, Kritschgau claims, was forged from bio-materials and frozen into place over the course of a year. He insists Mulder was only meant to see the alien--to make him believe the lie. Mulder counters that it is Kritschgau who is the liar. But when Mulder returns to the warehouse, he discovers the dead bodies of Arlinsky and Babcock--and the alien specimen missing. Shortly thereafter, Scully tells him the men behind the hoax gave her cancer all in an effort to make him a believer in their lies. Mulder is stunned by the revelation.

     Back in the current day, Scully tells FBI officials that she received a phone call from the police department asking her to identify a body inside Mulder's apartment. Struggling to maintain composure, Scully reveals that Mulder died of an apparent self-inflicted gunshot wound to the head.