While Scully takes time off to deal with the early stages of her pregnancy, Doggett and Skinner attempt to avert the mysterious murder spree of a religious cult leader who kills his victims in their sleep.
Agent James Leeds sleeps peacefully in his car when Agent Angus Stedman knocks on his window. “Damn Jim, you fell asleep! We’re on a stakeout, man.” Stedman points out that the house’s front door is wide open and they had better check it out. They follow bloody footprints into a room full of dead people. They split up to check out the house.
Leeds hears gunfire and heads out to the atrium to find Stedman dead on the ground with the same wound as all the people in the room. Crouched over Stedman, Leeds hears a noise behind him and spins around just in time to see a man with three eyes bring an axe down on his head.
Dana Scully wakes up John Doggett with a phone call informing him that an agent surveilling a cult group has been found dead in Pittsburgh and so have all the cult members. Scully is calling to tell him she can’t be there but doesn’t explain that she is in the hospital.Upon his arrival Doggett meets Assistant Director Skinner who recounts the cult was being watched because of rumors about drug trafficking. Agent James Leeds is still in his car, dead with a deep wound in his head. No room for a weapon to be swung, car was still locked, and Leeds’ gun is holstered. All the cult members are dead from the same head wound except for their leader, Anthony Tippet, a convicted murderer who claimed he had found God. Another agent tells them they still haven’t found agent Stedman but Doggett knows him and suggests they check his condo, since Stedman was from Pittsburgh and kept a condo there. Skinner and Doggett break into Stedman’s locked condo and find him dead in his bed from the same wound as all the other people.
Skinner summarizes Tippet and so forth to Doggett, Director Kersh, and other members of the FBI. Tippet made a hybrid religion that preached the importance of following the twin aspects of the Holy Spirit, both light and dark. Get closer to God by going into the darkness through the use of a hallucinogen Tabernanthe Iboga (bark of a tree).
The cult followers were not on the drug when killed and there seems to be no forensic evidence which leads Skinner to suggest that Tippet succeeded in reaching a higher plane and his consciousness murdered these people. Director Kersh is infuriated by this answer and assumes that Scully came up with it but Scully had nothing to do with it.
A homeless man asks for change from Tippet on the street as he goes to a pay phone. Tippet grabs the man and tells him “you don’t want to know me!” Tippet makes a call to a man blaming him for what is happening. The man slices open his forehead in response to this.
Doggett identifies the murder weapon as a ceremonial axe used a thousand years ago and only in museums now. He wants Scully’s help on the case but Skinner insists that she needs this personal time off.
The homeless man encounters Tippet again. A three eyed Tippet that watches as the man is pulled into the concrete as if it were quicksand and then the axe falls…Skinner speaks with Doggett about the homeless man and the pay phone call log. This leads them to the associate of Tippet, Dr. Andre Bormanis with his x cut into his forehead. Bormanis has a lab with rats for testing and it seems to be meant for developing drugs. Bormanis admits to supplying Tippet and his cult with hallucinogens but only Tippet ever used them because only he was strong enough for it. Doggett and Skinner decide to bring Bormanis in.
While Doggett walks away from the cell, he sees bloody footprints which lead him to a hovering Tippet with three eyes. He finds himself holding the severed head of Scully before Skinner wakes him up with a phone call from her. Scully tells him that he should get some sleep and that he should talk to Mulder’s friends about this.
Skinner informs Doggett that the drug Bormanis was attempting to take while they were hauling him in was a super-amphetamine. Doggett realizes that Bormanis doesn’t want to fall asleep and that they need to talk to him now. Bormanis finds three eyed Tippet and sees rats swarm him and bite him to death for his experiments on them. Doggett and Skinner arrive in time to find Bormanis dead.
Doggett finds the Lone Gunmen in the X-Files offices. Lone Gunmen bring up the third eye idea, a concept from eastern religions suggesting that if you could open up your third eye (all people have one) that you would see a new reality that is closer to God. Doggett says Tippet believes he has opened his third eye and that he is attempting to destroy others’ third eyes. They suggest that Tippet makes his victims think they are going to be killed (a telepathic assassin) and then it comes true but Doggett doesn’t buy it. He does however believe that Tippet believes it so Doggett and Skinner go to Bormanis’s laboratory under the assumption that Tippet would need more of the drug.They find Tippet at a table saw, watching it hypnotically. Tippet says he can’t stop it. He slams his head into the spinning saw.
Doggett notices Scully is in the hospital when he signs the wounded Tippet in. After checking on her, he talks with Director Kersh and Skinner. Doggett says that Tippet thought he could get into peoples’ minds and make their nightmares real to kill them and Kersh says the case is over. Doggett angrily points out how there is no evidence to prove Tippet’s involvement. Kersh insists it is closed.Doggett calls Scully and then goes to sleep. When he wakes up he sees a third eye on his face while he dresses. He speaks with Skinner about how he is afraid he isn’t actually awake. "Last night I dreamt Tipet was inside my house holding an axe. I thought I woke up this morning. I thought I was awake, but-but then..."
He is visibly shaken and Skinner sends him home to get some rest.Doggett gets out of the elevator and finds an empty hallway. A hallway that then expands infinitely in both directions. Tippet arrives and tells him that Doggett will kill Scully. Doggett enters Scully’s apartment after it materializes but forces himself not to kill her in her bed with the axe that appears. Instead he brings the axe to his own face rather than kill her (he isn’t really in control of his actions). The axe head approaches. Scully wakes him up. She came through the unlocked front door to find him. Doggett says he would have died right there if she hadn’t woken him up. Scully informs him that Tippet died. Scully tries to convince him that it was a bad dream but nothing else…
- The title of this episode is Latin for "the negative way" or "the negative path."
- When Agents Doggett and Skinner first confront Dr. Andre Bormanis they flash their badges. Skinner holds his upside down.
- David Duchovny (Fox Mulder) does not appear in this episode, but Mulder is mentioned.
- When Doggett takes a look at Tippet's Department of correction file you can see that there is a misprint under the name, alias is written alais.
- Apparently the Lone Gunmen were in a little over their heads - Langly had just told Agent Doggett he was in way over his head - as John Byers said the "Third Eye" is called the "Sahasrara", when it is actually known as the "Ajna" Chakra.
- Keith Szarabajka as Anthony Tipet
- James Pickens, Jr. as Deputy Director Alvin Kersh
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- Kirk B.R. Woller as Agent Gene Crane
- Grant Heslov as Dr. Andre Bormanis
- Wayne Alexander as Agent G. Arnold
- Kevin McClatchy as Agent James Leeds
- Lawrence LeJohn as Agent Angus Stedman
- Wayne A. King as Homeless Man
- Christopher Jacobs as ER Doctor
- Mary Ostrow as Nurse McCaslin