A computer hacker nicknamed The Thinker gains access to top secret Defense Department files on extraterrestrial life. He gives Mulder the files on a computer diskette with one provision -- that government officials be held responsible for UFO cover-ups throughout the years. Mulder's initial enthusiasm is dampened when he realizes the files are encoded in Navajo. Scully promises to find a translator as soon as possible. When Skinner questions Mulder about the rumor he possesses sensitive information, Mulder suddenly punches him. Mulder is at a loss to explain his inexplicable behavior. Skinner later informs Scully that a disciplinary hearing will determine if Mulder is to be dismissed without reinstatement.

The Cigarette-Smoking Man pays Mulder's father an unexpected visit on Martha's Vineyard. He informs him about the top secret files falling into his son's hands. Mr. Mulder realizes his name is on those files. He telephones his son and asks him to come home. Later, Scully lets herself into Mulder's apartment when he fails to answer his door. Suddenly, a gunshot rings out, smashing a window. Scully narrowly avoids injury.

When Mulder arrives at Martha's Vineyard, his father speaks cryptically about his work for the State Department. Before he can explain the truth, Alex Krycek shoots and kills him. When Scully learns of the killing, she urges Mulder to leave Martha's Vineyard less the authorities suspect him of the murder. When Mulder returns home, he is very ill. Scully attends to his sickness. She notices a suspicious delivery person carting a soft water canister to the basement of the apartment building.

Mulder spots Alex Krycek sneaking around outside his apartment building. He wrestles the agent to the ground and grabs his revolver. Certain that Mulder is about to kill Krycek, Scully draws her weapon and shoots Mulder in the shoulder.

When Mulder regains consciousness, he is lying in a motel room in New Mexico, his bullet wound having been attended to by Scully. She explains that lab tests revealed that water flowing into Mulder's apartment building was spiked with a strong hallucinogen, explaining Mulder's aggressive behavior.

An Indian man named Albert Hosteen begins translating the encoded Defense Department files. He explains to Mulder how a tribe of Indians who once lived in New Mexico disappeared without a trace. Their name was Anasazi, which means Ancient Aliens. Albert believes they were abducted by visitors from another planet. Albert's nephew Eric leads Mulder out into the desert. There, Eric shows the agent a railroad train boxcar buried in a rock quarry. Inside the car are the corpses of what appear to be alien beings. The Cigarette-Smoking Man calls Mulder on his cellular phone, claiming that Mulder's father authorized the project. Mulder insists he will expose the Cancer Man. The Cigarette-Smoking Man traces Mulder's location by pinpointing the source of the cellular phone transmission, but when he arrives in the desert by helicopter, Mulder is not to be found. The CSM orders his men to destroy the boxcar.