Special Agent Dana Scully, a medical doctor and instructor at the FBI Academy in Virginia, receives instructions to report to Chief Scott Blevins in Washington. Blevins assigns Scully to investigate--and debunk--an unassigned project dubbed "The X-Files," a burial ground for mysterious, unsolved FBI cases linked to the paranormal.

Scully is instructed to contact Fox Mulder, an agent who has become obsessed with investigating the otherwise forgotten X-File cases. Mulder displays a particular interest in a series of mysterious deaths scattered across the United States linked by one common clue: two strange red marks on the victims' skin.

Mulder and Scully fly to Bellefleur, Oregon, to investigate the death of Karen Swenson, a high school student who died mysteriously, and whose corpse is marked with two red welts. The agents exhume the body of Ray Soames, one of Karen's classmates. When Soames' casket is opened, however, a strange humanoid carcass is discovered inside. The corpse turns out to be that of an orangutan, and X-rays reveal an unidentified metal object implanted in the creature's nasal cavity.

Mulder and Scully question Billy Miles and Peggy O'Dell, classmates of Swenson and Soames who were injured in an automobile accident and have since been institutionalized. Miles has been reduced to a near vegetable state, while O'Dell has been confined to a wheelchair. O'Dell suddenly becomes violent, and in the struggle to subdue her, two red marks are discovered on her skin.

While searching the field where Karen Swenson met her fate, the agents are confronted by a detective who orders them off the premises. The pair comply, but as they drive along the highway, they are blinded by a strange light from the sky. The light drains the energy from their car, bringing it to a halt. Mulder looks at his watch and realizes nine minutes cannot be accounted for.

The pair return to their motel where Mulder tells Scully that his interest in the X-Files stems from his childhood when his sister, who was then eight years old, was abducted from their bedroom while he slept. Mulder says that he could not recall any of the incident until placed under hypnosis years later.

An anonymous phone call tips the agents that Peggy O'Dell was killed as she ran along the highway. While investigating the incident, the agents are informed that the autopsy bay was vandalized. They return to the hotel to find their rooms have been set ablaze, destroying all evidence gathered in the case.

The agents are confronted by Theresa Nemman, daughter of the coroner who originally performed the autopsies on the victims. She admits she too bears the red marks on her skin, and describes how a bright light appeared in the sky the evening she was hanging out with her friends Billy Miles and Peggy O'Dell.

Mulder hypothesizes that Billy Miles is under the control of an alien force. He adds his belief that Billy killed Peggy O'Dell. The agents return to the forest hoping to gather more evidence. Detective Miles attempts to stop them, and both he and Mulder witness Billy carrying Theresa to the spot in the woods where the other bodies had been found. A mysterious light illuminates Billy, and a strong wind swirls around him. Moments later the light fades and the winds die, and Billy stands over Theresa not knowing where he is or how he got there. The welts having vanished from his skin.

After returning to Washington, Scully gives her report. Much to the surprise of her supervisors, the metal object removed from the corpse was not destroyed with all of the other evidence. Scully kept it on her person and turns it into them as the single remaining piece of physical evidence of what had transpired. The metal object is taken by The Cigarette-Smoking Man and filed away alongside several others inside a massive government warehouse in the basement of the Pentagon.