S1E3 · Squeeze

In Baltimore, businessman George Usher arrives at his office building. He is watched from a storm drain by someone who then infiltrates the building by climbing through the elevator shaft into the ventilation system, kills Usher and removes his liver.

Usher's murder, the latest of three, is assigned to careerist FBI agent Tom Colton (Donal Logue), who turns to Dana Scully (Gillian Anderson) for help. Colton is baffled by the lack of entry points at the crime scenes and by the apparent removal of the livers with bare hands. Fox Mulder (David Duchovny) notes their similarity to earlier murder sprees from 1933 and 1963. At the scene, he notices an elongated fingerprint on the air vent, which he finds to be similar to some documented in the X-Files. He concludes that because five murders occurred during the earlier sprees, the investigators should expect two more.

Because Scully believes that the killer will return to the scenes of his earlier crimes, she and Mulder wait in the parking garage of the office building. There, they catch a man named Eugene Victor Tooms (Doug Hutchison) climbing through the air vents. Tooms is given a polygraph test, which includes questions written by Mulder linking him to murders dating as far back as 1903. Tooms passes most of the test, but crucially fails Mulder's questions placing Tooms at the historical murders. However, Colton dismisses Mulder's queries and lets Tooms go. To prove his assertion to Scully, Mulder digitally elongates and narrows Tooms' fingerprints, showing that they match the prints at the crime scene. He believes that Tooms is able to stretch and squeeze his body through narrow spaces. That night, Tooms demonstrates this ability by squeezing down a chimney to claim another victim.

Mulder and Scully find no documentation on Tooms' life. They visit retired detective Frank Briggs (Henry Beckman), who recounts his investigation into the 1933 murders. Briggs brings out old photographs of Tooms—who has not aged in sixty years—and gives them the address of Tooms' former apartment building. There, Mulder and Scully find a "nest" constructed out of newspaper and bile in the building's crawl space, as well as several trophy items taken from past victims. Mulder suspects that Tooms is a mutant who can hibernate for thirty years at a time after consuming five human livers. As the two leave, Tooms, who is hiding in the rafters, stealthily takes the necklace Scully is wearing as a new trophy.

Mulder and Scully put Tooms' apartment under surveillance, but Colton has them taken off the job. Mulder finds Scully's necklace inside the apartment and tries to call his partner, but her phone line has been cut. Tooms breaks into Scully's apartment through a tiny air vent to kill her, but Mulder rushes there and apprehends him first. Tooms is institutionalized and begins to build another nest using newspaper. Scully informs Mulder that medical tests on Tooms show an abnormal skeletal and muscle system, and a rapidly declining metabolism. When Tooms is given food through a slot in the door, he stares at the thin slot and grins.