Mulder and Scully discover evidence of a supersecret government experiment involving extraterrestrial DNA. When Mulder disappears, his partner has no choice but to turn to his mysterious informant, Deep Throat.

A car chase ensues with a mysterious man being followed by the police all the way to the docks. The man is trapped so jumps into the river after having been shot several times and when the cops rush up there they discover a trail of green blood.

Mulder asleep is woken up by a phone call from Deep Throat where he tells him to turn over to Channel 8. He turns over and sees the news reporting the incident. He goes with Scully down to the docks where they find a car which does not match the one shown on the news. They trace the car to a Dr. Berube who turns out to be very uncooperative. Scully thinks that Deep Throat is 'toying' with him so he arranges another meeting with him where Deep Throat tells Mulder to persevere with the case as he says "You've never been closer".

Meanwhile, the Crew-Cut man murders Dr.Berube. The agents examine the crime scene and find an erlenmeyer flask with the words 'Purity Control' written on the bottom. Mulder is intrigued by this so he gets Scully to take a sample down to a Dr. Carpenter who tells her that Dr. Berube has been cloning alien bacteria each containing a virus. She also tells her that the samples contain a fifth and sixth nucleotide which do not exist in DNA so they would have to be extra-terrestrial.

Later Mulder is contacted by the fugitive who is traced to a warehouse named 'Zeus Storage'. Mulder opens the door and finds a room with five tanks each containing a human body suspended in solution. As he leaves, he is chased by a murderous group of armed men but he manages to escape. Scully contacts Mulder and apologizes telling him that she has never believed that anything can go beyond the realms of Science. Mulder then shows Scully the warehouse he located but it is now empty. Deep Throat shows up telling them that the men were all part of an experiment using alien viruses to test on them. He also tells them that the fugitive who is named Dr. Secare is one of those experiments and that they must find him before government officials do.

The agents both separate now. Scully returns to Dr. Carpenter but learns that she has recently been killed in a car crash while Mulder locates Dr. Secare only for him to be killed by the Crew-Cut man and for Mulder to be taken hostage. When Scully learns that Mulder is missing she is told by Deep Throat that the only way to release Mulder is to access a high security storage facility and take an alien fetus which she does. Deep Throat and Scully meet with the Crew-Cut man on a bridge while Deep Throat hands over the fetus in exchange for Mulder's safety. Mulder is let go but Deep Throat is shot and killed by the Crew-Cut man his last words being "Trust no one".

Two weeks after the incident, Mulder rings Scully telling her that the X-Files have been shut down and that they have been reassigned to other sections. As we see in the Pilot episode, Cancer Man enters a Pentagon storage facility and places the fetus in a box as he walks down the spooky corridors locking the door as he leaves....