Agent Dana Scully is assigned to work with Agent Fox Mulder on the X-Files in an attempt to debunk his work on the paranormal. Their first case has them investigating apparent alien abductions. A near comatose man, Billy Miles, is taking his classmates, including Theresa Nemman, into the woods, where they are killed in a flash of bright light.

Mulder and Scully travel to Idaho to investigate the disappearance of a military test pilot. They observe unusual aircraft activity, prompting Mulder to proclaim the existence of a government conspiracy. Mulder sneaks onto the military base and is spotlighted by one of the craft, but is captured by soldiers and has his memory erased before he is released.

Mulder and Scully investigate a series of murders where there appears to be no tangible method for the murderer's entrance and escape. Eugene Victor Tooms, a seemingly normal janitor, is suspected by Mulder to be a mutant who kills his victims and extracts their livers in order to prolong his existence.

Mulder becomes obsessed with solving a case that closely parallels an "encounter" he experienced as a child.

Mulder and Scully track a legendary creature that has roamed the New Jersey countryside for over 40 years.

On Halloween, Mulder and Scully investigate the death of a corporate executive who may have been murdered by a thinking computer.