S2E25 · Anasazi

In the desert on a Navajo Indian reservation in New Mexico, a teenage boy comes across a boxcar buried in the ground. He retrieves the corpse of an alien-like figure from the boxcar, which he takes back to the reservation and presents to the residents, including a Navajo elder named Albert Hosteen.

Shortly afterward, Kenneth Soona, a computer hacker known as "The Thinker", breaks into the Defense Department database and downloads secret files related to extraterrestrial life, putting them onto a digital tape. When the Syndicate, a secretive group of government officials, learns of the breach, the Smoking Man tells them that he has already resolved the matter, although this is a lie. The Lone Gunmen visit Mulder and inform him that Soona wants to meet with him, but are interrupted by the sound of a gunshot. When Mulder goes out to his apartment hallway to investigate, he finds that one of his neighbors has shot her husband.

Soona gives the digital tape to Mulder at a discreet meeting in a park. An excited Mulder returns to FBI headquarters, only to find that the tape is encrypted. Scully believes the encryption is based on the Navajo language and takes the tape in order to investigate. When Skinner calls Mulder to his office to question him about the tape, Mulder voices his disdain for recent case assignments and his personal belief he has recently been used to “do the government’s dirty work”. The confrontation escalates to the point where Mulder assaults Skinner. Scully is brought before an FBI panel led by Skinner and is questioned about Mulder's actions. Scully is told that Mulder faces dismissal from the FBI, and that she will suffer a similar punishment if she has lied to them.

On Martha's Vineyard, the Smoking Man visits Mulder's father, Bill, and informs him of his son's likely possession of the tape. Scully meets with a Navajo translator, who refers her to a code talker. Mulder is called away to see Bill; when Scully arrives at his apartment, she is grazed by a bullet shot through his window. When Mulder arrives at Bill's residence, his father prepares to reveal the truth about everything, but is shot and mortally wounded by Alex Krycek. When Mulder contacts Scully, she tells him to flee the scene. After Mulder arrives at her apartment, Scully takes his gun from him while he sleeps.

Scully brings the gun to the FBI for comparison against the bullet that killed Bill. When Mulder awakens, he becomes angry and suspicious towards Scully. Returning to Mulder's apartment, Scully finds his water is contaminated. As Mulder enters his building, he spots Krycek, whom he disarms and prepares to kill. Scully shoots him to prevent him from doing so, allowing Krycek to escape. Scully brings an unconscious Mulder to New Mexico. When Mulder awakens, Scully reveals that his behavior was caused by a drug placed in his water supply. She shot him because if he had killed Krycek, it would have been harder to prove his innocence in his father's death. She introduces him to Hosteen, who has been translating the files on the tape.

Scully reveals that the tape contains information on both her and Duane Barry. Hosteen introduces Mulder to his grandson, who drives him to the buried boxcar. Just before Mulder heads in, he is called by the Smoking Man, who is able to trace Mulder's location through the call. Mulder heads inside the boxcar and finds a pile of the dead creatures, each with smallpox vaccination scars on their arms. The Smoking Man arrives by helicopter with eight armed commandos and, not finding Mulder inside, orders the boxcar to be burned.