Gary Kane, a sixteen-year-old high school student, leaves his home suddenly after receiving a mysterious phone call. When Gary fails to return home, his mother, Beth, notifies police. Two officers on patrol notice Gary-who is clad only in his underwear-wandering aimlessly in a wooded area. A phrase is written on his back in marker: "He is one."
     Mulder and Scully review the facts in the case. Gary was not sexually assaulted, nor was he the victim of a prank. Surprisingly, there are reports of other teenagers having experienced similar ordeals. Mulder's curiosity is piqued when a Wisconsin sheriff, Bill Mazeroski, speculates that the victims have been possessed. He explains that a religious cult called the Church of the Red Museum settled into the area and purchased a cattle ranch. Being vegetarians, the church members turned beef cattle into pets-much to the consternation of local ranchers. The sheriff takes the agents to the church. They watch as Richard Odin, the sect's leader, addresses his parishioners via a computer. Mulder explains to Scully that the church members are "walk ins"-believers in soul transference who have taken possession of other people's bodies.
     Local teenagers harass a young Red Museum member. Mulder comes to the boy's aid, and in the process learns that one of the harassers is the sheriff's son, Rick. A girl who participated in the verbal attack on the Red Museum member is later found with the message "She is one" scrawled on her back. Lab tests reveal large quantities of a hallucinogen-a controlled substance-in the girl's blood. That night, a small plane carrying Dr. Gerry Larson crash lands in a field. Mulder, Scully and Sheriff Mazeroski discover a briefcase bearing Larson's initials filled with hundred dollar bills. They also discover a vial containing a mysterious fluid, and a computer printout list containing the names and credit card numbers of the victims' families... each of whom Larson delivered and treated through childhood.
     While interviewing Beth Kane, Mulder notices a light shining through a hole in her bathroom mirror. He smashes the glass, revealing a video camera surveillance set-up. The man behind the surveillance, Gerd Thomas, abducts Rick, the sheriff's son... just as he abducted all the previous victims. But instead of turning up dazed, Rick is found dead. Mulder discovers that Gerd Thomas owns the building where the Kane family lives. He is placed under arrest. Numerous video tapes are recovered. Thomas apologizes for his sickness but insists he did not murder Rick. He explains that Dr. Larson was paying him to inject cattle with a mysterious liquid... the same liquid Larson used to "inoculate" his young patients.
     Scully sees the mysterious Crew-Cut Man--who executed Deep Throat--driving on the street. Mulder realizes that the mysterious fluid is alien DNA, the same substance found in the erlenmeyer flask months earlier. The Crew-cut Man, Scully speculates, killed Rick to cover up evidence. Aware that other lives are in danger, Mulder asks the sheriff to round up everyone on Larson's computer list and transport them to the Red Museum. Realizing that the Crew-cut Man's base of operation is the local slaughterhouse, Mulder rushes to the scene. He finds the facility soaked with gasoline. The Crew-cut Man suddenly springs from the darkness and a fight ensues. Scully and Mazeroski arrive and shoot the Crew-cut Man, killing him. An investigation reveals no clues as to who the man was or the chemical makeup of the substance injected into the townspeople.