Mulder experiences a dreamlike vision, apparently a memory from childhood, in which he sees his mother and father reacting as if some terrible tragedy has entered their home. Mulder awakens in a motel room, sweating profusely, his hands and shirt stained with blood. He telephones Scully, who drives to the motel to offer assistance. Suffering from a mental blackout, Mulder cannot recall how he got to the motel. Scully discovers that two rounds were fired from his gun. She also traces a car parked outside Mulder's room to a David and Amy Cassandra. The agents travel to the Cassandra residence, where they speak with a house-keeper. Inside the home are dozens of paintings of a white clapboard house. Mulder realizes he was inside the home, but cannot remember why.

The housekeeper gives the agents the address of the home depicted in the painting. As Mulder approaches the dwelling, he is suddenly struck by a flashback in which he encounters a young Cigarette-Smoking Man inside his parent's home. When the seizure subsides, the agents walk inside the cottage, where they find the dead bodies of David and Amy Cassandra.

Blood from both victims is found on Mulder's shirt. Detective Curtis places Mulder under arrest. But a toxicology report reveals traces of the anesthetic Ketamine in Mulder and Amy Cassandra's blood. Scully realizes the drug could account for Mulder's memory loss. A short time later, Michael Fazekas, an admitting officer, steps inside a bathroom at the police station and shoots himself in the head. Scully discovers a small scab on the man's scalp, similar to one found on Amy's hairline. Detective Curtis reveals that Fazekas was a believer in UFOs. Inside Fazekas' apartment, Scully discovers a UFO magazine featuring a photograph of Amy, who believed she was an alien abductee.

A forensics report reveals that the blood spatter pattern on Mulder's shirt does not correspond to the point of entry detail. Curtis concludes the Cassandras died as the result of a murder-suicide. Further research reveals that Amy had been seeing Dr. Charles Goldstein, a psychiatrist, in an effort to recover suppressed memories. Goldstein admits he used unconventional therapy to stimulate electrical impulses in the brain.

Mulder suffers another seizure. During the attack, he experiences a vision in which a young Cigarette-Smoking Man pulled Mrs. Mulder close to him, as if to kiss her. Mulder and Scully drive to Mrs. Mulder's Greenwich home. There, Mulder confronts his mother. He accuses her of lying to him about having been forced to choose Samantha over him. He also accuses her of being unfaithful to his father. Mrs. Mulder angrily denies the allegations. Mulder storms out of the house and drives off.

Mulder pulls a gun on Dr. Goldstein and forces him to finish his treatment--to make him relive (what he believes to be) to his past. Goldstein drugs Mulder, then slowly lowers a spinning needle towards his hairline. Police arrive at the scene and place Goldstein under arrest, but Mulder's whereabouts are unknown. The psychiatrist tells Scully that Mulder left his office "to exorcise his demons." Scully finds him at the house in Quonochontaug, balled up on the floor, a gun in his hand. Jolted by seizures, Mulder aims his gun at Scully. She attempts to convince him that the powerful hallucinogen injected into his body has affected his mind and that his visions, his apparent memories, cannot be trusted. Mulder fires a shot, but the bullet shatters a wall mirror behind Scully. Breaking down into tears, Mulder lowers the weapon. Scully's fear changes to sympathy as she comforts her partner.