VIA NEGATIVE

In Pittsburgh, two FBI agents, Angus Stedman (Lawrence LeJohn) and James Leeds (Kevin McClatchy), are observing a house when Leeds falls asleep. When he awakes, he discovers that the front door of the house is open. The two agents investigate and stumble upon a room filled with dead bodies. Suddenly, a man wielding an axe and possessing a third eye murders both agents with a blow to the head.

The following day, Dana Scully (Gillian Anderson) calls John Doggett (Robert Patrick) to inform him about the case and says she will not be joining him, due to personal matters. Doggett visits the crime scene, where he meets up with his boss, Walter Skinner (Mitch Pileggi). Skinner tells him about the cult and how the victims died. Leeds' body is found in his car, but his partner, Stedman, is missing, along with cult leader Anthony Tipet (Keith Szarabajka): the man with the third eye. The FBI later finds Stedman at his locked-up condo with a fatal blow to the head. Meanwhile, Tipet is searching for a pharmacist and stumbles into a phone booth to call an unnamed person. When a tramp asks him for change, Tipet attacks the tramp, trapping him in the pavement and axing his forehead.

At the FBI, Skinner briefs Alvin Kersh (James Pickens, Jr.), and other agents about the case. He tells them that Tipet used a hallucinogen Tabernanthe iboga to bring himself closer to God using a combination of Christian and Eastern religious practices called the via negativa, meaning the "negative way" in Latin. Tracing Tipet's earlier call leads Doggett and Skinner to Andre Bormanis (Grant Heslov), a drug dealer. Bormanis is arrested, and put in a cell at the local police department. At the jail, Doggett has a vision of him holding Scully's severed head in his hands. After waking, Doggett realizes his vision was a bad dream. Meanwhile, in his cell, Bormanis has fallen asleep, and is dreaming of being attacked by rats. Doggett and the other officers find Bormanis' gnawed-up body.

Doggett returns to the X-Files office, where, to his surprise, he meets The Lone Gunmen. They tell him about the history of the third eye. While coming to the same conclusion, they are convinced that Tipet is projecting himself into people's dreams and killing them there. Returning to the warehouse where they found Bormanis, Skinner and Doggett meet Tipet, who is trying to take his own life by pushing his head through a table saw. They rush him to the hospital, where Doggett by surprise finds Scully's name on the register. With Tipet in a coma, Kersh decides to pull the plug on the case, saying they've found the main suspect. But Doggett and Skinner are not satisfied, saying there are no explanations for the various murders and events surrounding the case.

The next day, Doggett wakes up and discovers that he now has a third eye in the middle of his forehead. Suddenly, it vanishes. At the FBI building, he talks to Skinner, hoping for reassurance. He expresses his fear that, despite Tipet being in a coma, Tipet may still be able to enter into his dreams. Skinner, however, dismisses his concerns and sends him home. While leaving, Doggett has a hallucination of Tipet, ordering him to kill Scully. Suddenly, Doggett finds himself in front of Scully. Rather than kill his partner, he turns the axe upon himself. Doggett is immediately awakened from his dark reverie and finds himself in his bedroom, with Scully standing over his bed. He begins to thank her for saving his life, but she informs him that Tipet died due to his coma

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