In the 1950s, two FBI agents investigate strange deaths somehow linked to Mulder's father.

In the year 1990, a sheriff escorts a landlord into a boarded-up, dilapidated house for the purpose of evicting the tenant, Edward Skur. Once inside, the pair smell a terrible odor, then discover a human body, collapsed, as if all of the internal organs have been removed. A figure springs from the shadows and the sheriff opens fire. The attacker, an elderly man, falls to the ground, mortally wounded. His last words are, "Mulder... Mulder."

FBI Agent Mulder, still a year away from working on the X-Files, pays a visit to a man named Arthur Dales. Mulder questions Dales, a former special agent with the Bureau, about his work on an unsolved case from 1952... one focusing on Edward Skur (the attacker from the opening teaser). According to the censored report, Skur disappeared 38 years earlier before he could be arrested for a series of killings in which the victims' internal organs were removed. When Mulder utters his own last name, a flash of recognition passes on Dales' face. Dales makes cryptic reference to HUAC, and the communist witch hunts of the 1950s, prompting Mulder to review newsreel footage of the McCarthy hearings. While watching the tape, Mulder notices his own father sitting amidst McCarthy's group. When Mulder returns to Dales' apartment, Dales elaborates on Skur, who, years earlier, was labeled a communist.

The story flashes back to 1952. A young Ed Skur is arrested by FBI agents Dales and Michel, and charged with contempt of Congress for failing to appear before the committee. That night, Dales relaxes at a bar called the Hoot Owl. He receives a phone call from his partner, informing him that Skur hanged himself inside his jail cell. Dales travels back to the Skur residence to inform the family of the death. But before he exits his car, he sees Skur walking down the street. An incredulous Dales gives chase. A struggle ensues, during which black tendrils creep out of Skur's mouth. The fight attracts attention, and Skur runs off.

Dales files a report about the farfetched incident. Shortly thereafter, he is summoned to the office of Special Assistant Roy Cohn. Cohn tells Dales to amend the report by removing any reference to Skur. Dales does as he is told. A short time later, he and Michel are dispatched to a homicide. They discover the body of a dead German doctor, his body flattened. Dales notices a coaster from the Hoot Owl, on the back of which is a message: "come alone." That night at the bar, Dales is approached by a young Bill Mulder. He explains that it was he who summoned the agents to the doctor's home. He confirms that Skur is the perpetrator. He also explains that Skur is not a communist, but a patriot. Skur, along with two other men, Gissing and Oberman, worked for the State Department. Gissing and Oberman both took their own lives. Skur was arrested, and his death faked, so that the government could cover-up what it had done to him. Bill Mulder wants the truth to be known, explaining that Skur was a colleague. But he warns that Skur believes that Dales and Michel are part of the conspiracy against him. Shortly thereafter, Skur attacks Michel. A spider-like creature crawls from Skur's mouth and enters Michel.

Cohn orders that Michel's body be transported to Bethesda instead of allowing a county coroner to perform the autopsy. Dales protests until Cohn threatens to label him a communist. When Dales returns to the Bureau, he notices a heavily-censored document on the desk of Dorothy Bahnsen, a clerk. Dorothy explains that the document is a deposition that branded Skur and his co-workers communists. She then states that she recognized one of the men named in the document from an X-File. She explains that an X-File pertains to unsolved cases and that only the director's office decides which file is designated with the "X." She pulls out the file on the man whose named she recognized. It belongs to a German immigrant, Dr. Strohman. Dales recognizes Strohman as the man found inside the house. Dales tracks down Gissing's body and supervises an autopsy. Inside the corpse is a cocoon containing a spider-like creature, which Dales kills. Later, Dales informs Mrs. Skur that her husband, along with two co-workers, was tricked by the government. He elaborates, explaining that all three men underwent surgery for treatment of war injuries, but, in reality, received an operation called xenotransplantation the grafting of a species into the human body. That night, Bill Mulder and Cohn's assistant escort Dales to the bar where he is scheduled to meet Skur. Dales is equipped with a hidden microphone and told that Skur will be arrested the moment his guard is lowered. Later, Skur enters the empty bar. He tells Dales the other men will not be coming, explaining that they assumed he (Skur) would kill him.

Dales sees the logic of Skur's words. A struggle ensues, during which Dales is able to handcuff Skur to the bar. Back in 1990, Dales finishes telling his story to Mulder. But the puzzle still remains: why did Skur die saying the name of Mulder's father? The story then flashes back to 1952... when a young Bill Mulder stopped on a road and gave Skur the keys to his handcuffs.