S1E1 · Pilot

Outside the Oregon town of Bellefleur, teenager Karen Swenson is seen fleeing through the forest at night. When she falls, a dark figure approaches, and they both become enveloped in light. Swenson's body is later found by Bellefleur detectives, with two small marks on her lower back.

Later, in Washington, D.C., FBI Special Agent Dana Scully (Gillian Anderson) is summoned to a meeting with Division Chief Scott Blevins (Charles Cioffi). She is reassigned from her teaching position to work with fellow Special Agent Fox Mulder (David Duchovny) on the " X-Files ", an obscure FBI section covering unexplained phenomena. Blevins makes it clear to Scully that he expects her to discredit Mulder, regarded by his superiors as a gadfly.

Scully introduces herself to Mulder, who shows her evidence from the Swenson case. He notes that Swenson was the fourth member of her high school class to die under mysterious circumstances. He also notes an unknown organic compound found in the tissue surrounding the marks on her body, as well as similarities between her death and others from across the country. Mulder believes that Swenson's death is due to extraterrestrial activity. However, the skeptical Scully expresses disbelief in Mulder's theory.

When Mulder and Scully's plane flies over Bellefleur, it encounters unexplained turbulence. As they drive through the woods near the town, the agents' car radio goes haywire; Mulder marks the spot of this event by spray-painting an "X" on the road. Mulder arranges for the exhumation of the third victim, Ray Soames, despite the protests of Dr. Jay Nemman, the county medical examiner. When Soames' coffin is opened, a desiccated, malformed body is found inside, which Scully concludes is not Soames, but possibly an orangutan. She finds a grey metallic implant in the body's nasal cavity.

Mulder and Scully visit the psychiatric hospital where Soames was committed before his death and meet two of his former classmates—the comatose Billy Miles (Zachary Ansley) and wheelchair-using Peggy O'Dell. O'Dell suffers a nosebleed and is seen to have marks similar to Swenson's. Outside the hospital, Mulder explains to Scully that he believes Miles, O'Dell, and the victims to be alien abductees.

That night, the agents investigate the forest; Scully discovers ash on the ground, leading her to suspect cult activity. However, a local detective arrives and orders them to leave. Driving back to their motel, Mulder and Scully encounter a bright flash of light, and their car loses power at the same spot where Mulder had earlier spray-painted the "X." Mulder realizes that nine minutes have disappeared after the flash, a phenomenon reported by alien abductees.

At the motel, Mulder tells Scully that his sister, Samantha, suddenly vanished when he was twelve years old, which has driven his efforts to investigate paranormal cases. The agents receive an anonymous call to inform them that O'Dell has died. At the scene, they are informed that she was killed running into traffic and realize that she was killed at the exact moment they had experienced the flash on the road. Mulder is informed that the desiccated body has been stolen from the morgue. The agents return to their motel to find it ablaze, and all their evidence destroyed.

Nemman's daughter, Theresa, contacts the agents for help. She tells them that she has awakened in the middle of the woods several times, fears for her life, and admits to having the same marks; she also develops a nosebleed. Nemman and the detective, revealed to be Billy's father, arrive and take her away. The agents wonder about the bodies of the first two victims and return to the cemetery; they find the graves already dug up and the coffins missing. Mulder realizes that Billy is responsible for bringing the victims to the woods. There, they again encounter Detective Miles but hear a scream. Mulder and Detective Miles find Billy nearby with Theresa in his arms. There is a flash of light, and Billy and Theresa are recovered unharmed.

A couple of weeks later, Billy is put under hypnosis. He recalls how he and his classmates were abducted in the forest as they celebrated their graduation. The teenagers had been subjected to tests by the aliens and were killed when the tests failed. Scully provides Blevins with the metal implant, the only remaining piece of evidence. She later learns from Mulder that Billy's case files are missing.

The episode ends with an unnamed agent (William B. Davis), seen at the beginning in Scully's briefing with Blevins, storing the implant amongst other identical ones in a vast evidence room within the Pentagon.