A drug-worshipping cult goes postal, and Scully's in hospital...
FBI Agents Jim Leeds and Angus Stedman are watching a house. Leeds falls asleep, and wakes to find the front door of the house open. The Agents investigate, to find a room full of bloody dead bodies, and an axe-wielding man with a third eye in the middle of his forehead.
Phoning Doggett from casualty, Scully tells him about the death of an agent watching a religious cult in Pittsburgh. She won't be joining him due to personal matters.
In Pittsburgh, Skinner fills in Doggett about the Ibogan Temple, a cult suspected of drug smuggling. The cult members all died from a single would to the forehead. Agent Leeds' body was found inside his car, but Stedman is still missing, along with the Cult leader, Anthony Tipet. Stedman doesn't stay missing for long - Doggett and Skinner find his body locked in his condo, with a fatal wound to the forehead.
Tipet, meanwhile, is looking for a pharmacist - who it seems has taken a razor to his forehead in his dark warehouse. His third eye open, Tipet attacks a tramp, trapping him and axing his forehead when the pavement turns to ooze.
Skinner briefs Kersh and other agents at the Bureau. Tipet was using hallucinogens to bring himself closer to God using the 'via negativa' - the dark path - but none of the victims had used drugs. News of the vagrant's murder leads to Andre Bormanis - a drug dealer associate of Tipet's whom he phoned from the crime scene. As Bormanis is arrested, he tries to take amphetamines. He is put in the cells.
In the jail, Doggett sees a set of bloody footprints. Tipet is floating three feet above the floor, his third eye visible. Looking down, Doggett sees he has Scully's severed head in his hands... Waking from the dream, Doggett realises he was asleep in the jail. He wonders if Bormanis was taking drugs to stay awake.
In his cell, Bormanis has fallen asleep, and is dreaming of being attacked by rats. Doggett finds his gnawed body.
Scully sends Doggett to the Lone Gunmen, who tell him about the mythology of the third eye. Doggett is convinced that Tipet is projecting himself into his victim's dreams. Returning to the warehouse with Skinner, they find Tipet pushing his head on to a circular saw. They rush him to hospital, where Doggett finds Scully's name on the register. With Tipet in a coma Kersh decides they've got their man, but Doggett is not satisfied - there is no explanation for the events outside Tipet's beliefs.
Next morning, Doggett sees a third eye on his forehead as he dresses for work - it vanishes, but he seeks Skinner for reassurance at the Bureau. He is afraid that he is asleep and, despite the coma, Tipet could still enter his dreams. Skinner tells him he's fine and sends him home, but Doggett has a powerful hallucination in which Tipet tells him Scully will die.
Doggett finds himself in Scully's apartment with a bloody axe in his hands. Rather than kill Scully in her sleep, he turns the axe on himself. Waking up, he finds Scully standing over his bed, and thanks her for saving his life. Scully tells him Tipet died in his sleep.