When a computer hacker breaks into the most secret files proving the existence of extraterrestrial life, Mulder and Scully's lives and jobs are put in danger when Mulder gains possession of the files and goes in search of the real truth.

In New Mexico, an earthquake occurs only to end as suddenly as it began. The next day, a young Native American man finds something in the earth, something that should never be discovered, a real alien corpse.

Meanwhile, somewhere in Delaware, a computer hacker breaks into the secret MJ files and promptly downloads all he can onto a digital tape. Learning of this, nearly all the International governments are alerted. When the Cigarette-Smoking Man receives a phone call describing the recent incident he says to his fellow elders, "Gentleman, that was the phone call I never wanted to get".

Mulder is later contacted by the Lone Gunmen in his apartment where they explain that the hacker who hacked the files is named The Thinker and that he has asked to meet with Mulder in a secret location. Before the meeting ends, a gunshot is fired in the hallway. It turns out one of the neighbours has killed his husband after being married for 30 years. "Weirdness" the Lone Gunmen reply.

The meeting takes place where Mulder gains possession of the tape only to discover that they are encrypted in Navajo, the only code the Japanese couldn't break. While Scully tries to track down someone who can help translate the files, Mulder meets with Skinner about the missing files only to end up punching him in the hallway. Scully is concerned about Mulder's strange behaviour but has to attend a meeting where her superiors warn her that Mulder is in danger of being dismissed. Scully is also in danger after telling lies at the meeting.

Meanwhile, Mulder's father meets with the Cigarette-Smoking Man where he informs Mulder's father that the MJ documents have been breached. If Mulder comes to him for the truth he is strongly advised to "deny everything". Worrying that Mulder is in danger, his father summons him to his home to confess all to him about his sister and about his mysterious past just in case anything happens to him in the near future. Before he can confess any important information, William Mulder is killed by a gunshot in his bathroom by Krycek who runs off after hiding in the shower.

Mulder calls Scully straight away, who tells him that someone tried to kill her at his apartment and that it looks like Mulder killed his father if he stays there considering his recent bizarre behaviour. Mulder arrives at Scully's apartment only to wake and find that his weapon and badge has gone. Mulder, angry and sick, rings Scully and tells her that he doesn't have her trust any more believing that she thinks he killed his father.

Scully, on her own and trying to find out why Mulder is acting so strangely, discovers at Mulder's apartment that his water is being drugged which explains the recent murder in his building and Mulder's actions. Later, Mulder encounters Krycek and is about to kill him with Krycek's gun when Scully turns up and shoots Mulder to prevent him from committing murder.

Mulder awakens in New Mexico where Scully introduces him to Albert Hosteen, a Navajo code talker who is translating the files for him. Scully tells Mulder that when he is able, Albert will take him to a place where he will finally find all the answers he is looking for and that Scully's name is mentioned in the files along with Duane Barry's.

When Mulder is well enough, he is taken by Albert's grandson to a quarry where he finds a boxcar buried in the ground. Just before he enters, the Cigarette-Smoking Man calls him asking for his location but he doesn't need it for as soon as he hangs up on him, the Cigarette man boards a helicopter to prevent Mulder from finding out what his father wanted to tell him. Mulder enters the car, and finds piles of alien bodies stacked floor to ceiling. Calling Scully, he tells her what he sees. Scully tells Mulder that in the files, it mentions about Axis power scientists who performed experiments on humans. Mulder notices a small-pox vaccination scar on the arms of the victims and comes to a startling realization. He responds, "Oh my god Scully, what have they done" just as the door is shut on him. The Cigarette-Smoking Man turns up and searches the boxcar but can't find Mulder. He orders his soldiers to set fire to the boxcar and as Albert's grandson looks in horror, the car explodes in flames with Mulder trapped inside.

To be continued....