The teenagers of a small cattle-ranching town have been disappearing, only to be found stripped and wandering the nearby woods, marked with the phrase "He Is One." Local authorities suspect the Church of the Red Museum, a vegetarian cult that has recently taken up residence. When one of the teens is found dead, however, the toxicology report reveals an unknown substance—one that Scully recognizes from a certain Erlenmeyer flask. Could the town be the staging ground for a sinister government experiment?
- Call-Back: to "The Erlenmeyer Flask"
- Cult: The titular Red Museum
- Hate Plague
- Mystery Cult: The Church of the Red Museum.
- No Control Group: Averted.
- The Peeping Tom: "Red Museum" features a man who secretly records everyone living in his building from inside their bathrooms. He's the only person who seems to know what's actually going on.
- Red Herring: A lot of them. The red-turban cultists, the kidnappings, the doctor's plane crash, the men inoculating cattle, the hallucinogenic sequences in the woods, the peeping tom None of them bear real significance for the resolution of the case. The episode even appears to be a Monster of the Week story, but it turns out to be connected to Myth Arc with no new significant clues.
- Romance-Inducing Smudge: Mulder and Scully decide to eat at a local rib restaurant. In the middle of talking about the case they're on, Mulder just reaches over with a napkin and wipes a smudge of sauce off of Scully's face. Though taken aback, Scully graces him with a shy smile.
- Slaughterhouse Fight