As a businessman prepares for a late night at the office, he is unaware that he is being watched. He works at his desk in the seemingly empty office building, just as the screws on the air conditioner vent slowly loosen - from the inside out. The man goes to get a cup of coffee, and when he returns, he is savagely attacked. Moments later, the man lies dead, as the screws of the vent tighten from the inside.
Scully has lunch with Agent Tom Colton, an old friend from the FBI Academy. They catch up on old friends, and we learn Colton is a rising star at the Violent Crimes Section. Colton teases her, asking if she has had any "close encounters of the third kind." He also asks for her help - on three murders in Baltimore, including the businessman from the teaser. All were found in seemingly locked rooms, and all the victims had their livers torn out, as if by a bare hand. Colton wants to solve the crimes, and asks for Scully's input. He tells her the case is his ticket up the ladder, and if she can help, "maybe you won't have to be Mrs. Spooky anymore."
Scully and Mulder arrive at the crime scene, where Mulder takes the opportunity to freak Colton out with a tangent on an alien's skin tone, suggesting that the term "little green men" should actually be "little gray men." Colton is immediately dismissive and begins describing his theories to Scully. Mulder, meanwhile, notices an odd, elongated fingerprint on the air conditioning vent. Colton dismisses the print as irrelevant, since the vent is too small for a person to fit through, and the vent is not loose.
Back at the office, Mulder shows Scully the print he lifted and shows that it matches a print from a 1963 murder scene in Baltimore, as well as a murder in the same area in 1933, and early fingerprints link him to a 1903 murder. Mulder tells Scully that every thirty years; there has been a series of five murders where victims had their livers removed: with three down, the killer has two more to go in this cycle. Scully is incredulous that Mulder is suggesting a 100-year old serial killer who is capable of overpowering and killing a healthy businessman.
Scully instead works on a profile of the killer, believing that he is able to gain entry to buildings because he is a uniformed employee. She also thinks he will return to the scene of the crime to recapture the thrill of the kill. Her recommendations are accepted, and the FBI stakes out the murder sites. Mulder crashes her stakeout, saying it is a waste of time as the killer will not return. Mulder hears a noise in an air vent, and races over to find a scared looking man in an animal control uniform emerging from the vent.
The man, identified as Eugene Victor Tooms, is in custody and is administered a polygraph test. He denies the murders, but seems flustered by a question to see if he is over 100 years old. Mulder says he requested that the question be asked. Tooms passes the test, but the results show he lied about being over 100. The agent in charge dismisses Mulder's theory, and Colton tells Scully that Mulder is insane.
Mulder shows Scully Tooms fingerprints and elongates them and they match the prints from the crime scene. Tooms follows a man home and squeezes through the chimney and attacks him. Mulder and Scully arrive at the crime scene and Colton intercepts them and tries to make them leave but Scully defends Mulder. Mulder finds another print on the fireplace and sees that something is missing from the home.
Back at the office, Mulder show Scully records that show a "Eugene Victor Tooms" has resided at his current address at Exeter Street since 1903. Scully believes that Tooms' grandfather was the first killer and that Tooms is following in his footsteps. Mulder points out that the elongated prints are 100% identical.
Lynne Acres Retirement Home, Baltimore, Maryland
Mulder and Scully go to visit Frank Briggs, the detective who investigated the 1963 and 1933 murders. Briggs says that in each murder, a trophy was taken by the killer. He remembers Tooms as a suspect, but he could never get enough evidence to close the case. Briggs shows Mulder and Scully a photograph of Tooms taken in 1963, and he has not aged a day.
The agents then go to Tooms' address and find that it is practically condemned. Inside, they find what appears to be a nest made out of newspapers and Scully realizes it is covered in bile. Mulder believes that Tooms is a "twentieth century genetic mutant." that hibernates for the 30 year period between crimes, emerging long enough to eat five livers to sustain him. As they leave, they are being watched by Tooms, who takes Scully's bracelet - he plans for her to be his next victim.
The agents plan to stakeout Tooms' home, but Colton calls off the agents assigned. Scully is furious and goes home, unaware that she is being followed by Tooms. Mulder goes back to Tooms' apartment and sees Scully's bracelet among Tooms' trophy collection. As he races across town to get to Scully's apartment, Tooms bursts from Scully's air vent and attacks her. She fights him off until Mulder arrives. The two overpower him and handcuff him.
Later, Mulder observes Tooms in his cell, and watches as Tooms, seemingly detached from reality, begins making another nest from newspapers. Scully says that preliminary tests show oddities in Tooms' metabolism and physiology. Mulder muses that even the most expensive, sophisticated security system is not enough to keep monsters like Tooms away. Later, an orderly brings Tooms his food, and slides it through a slot in the door. Tooms eyes the small opening, and smiles...