Mulder and Scully investigate the disappearance of a number of teenagers in which the only main suspects seem to be a small religious cult. The agents though discover an unexpected lead which leads them to the same conclusion as in The Erlenmeyer Flask.

A teenage boy goes out for '5' minutes but instead stays out for much longer. When the police are called in to search for him, they find him naked on the side of the road apparently shocked with the words "He is one" written on his back in black marker.

Mulder and Scully come in to investigate and it seems that there has been a number of teenage victims in the same area each with the same words on their backs. Sheriff Mazeroski thinks that a small religious cult is responsible named the Church of the Red Museum who believe in not eating meat and of possession which is what seems to be the explanation for the kid's strange behaviour at the moment. The agents travel there but cannot really find anything to pin them to the deaths.

Later at night, a teenage girl is also kidnapped and turns up in a forest suffering from hallucinations. She has the words "She is one" on her back. When she is tested, Scully finds a strange chemical in her blood which only doctors could have got their hands on. When they finds that the Red Museum's leader, Richard Odin used to be a doctor, they arrest him and take him into custody. He denies murdering the children. Meanwhile, the rest of the group assemble in the town to protest when the sheriff's son suddenly walks up to them pouring a bucket of blood all over them.

While this is happening, an old man directs Mulder and Scully to a farm where he shows the agents some farmers injecting a genetically engineered hormone into cattle. He claims that the hormone is responsible for seven rapes which happened in the last year.

Later, a plane crashes in the fields of the farm, the passenger of the farm being Dr. Larsen who delivered the sheriff's son. When Mulder discovers a whole briefcase containing cash Mulder remarks that he "may have been delivering more than babies". Dr. Larsen was also responsible for giving vitamin shots to the abducted teenagers since they were born.

Meanwhile, Deep Throat's killer, the Crew-Cut Man shows up again and shoots one of the men who was working on the farm injecting cattle. Later, the sheriff's son is also abducted and is later found dead. While Mulder is searching the home of the first abducted teen again, he discovers a strange light shining through a mirror in the hallway. When he breaks the glass he finds a "private movie theatre" in which someone was video-taping what the household family were doing. The old landlord of the house is found to be Gerd Thomas so Mulder and Scully arrest him. He says that because of Larsen's tests, the children have become monsters which is why he abducted them. During the interview, Scully gets the lab tests back on a DNA sample recovered from the crash and it is found to be "Purity Control" much to the disbelief of her.

Mulder realises the murderer is the Crew-Cut Man so he takes the surviving teens to stay safely in the company of the Red Museum and heads off to a meat-packing plant. Trying to catch the Crew-Cut Man without harming him, Mulder is about to be killed by him when the sheriff shoots Deep Throat's assassin killing him.

No-one knows the identity of the man killed and no light is shed on what the children were being injected with. Scully says at the close of the episode "The case remains open and unsolved". We are left wondering what was happening....