While Agent Scully leaves a message on Mulder's answering machine about what happened when she scanned the metallic implant found in Duane Barry, he mysteriously appears outside her home. He breaks in through her window, attacks and kidnaps her, taking car and her gun as well. Soon after, Mulder arrives home and checks his messages. He hears Scully's message cut short by a window breaking and her screaming for help. He arrives at Scully's home and discovers that police have already established a crime scene. Scully's mother arrives, demanding to see her daughter's apartment and meets Mulder. She tells him that she had come because of a recurring dream in which Scully is taken away from her. Mulder looks down to find blood on his hand (which he accidentally touched previously).
The next morning at F.B.I. Headquarters, A.D. Skinner briefs everyone on the search for Duane Barry and Agent Scully. Shortly after, Skinner takes Mulder off the case and orders Krycek to take Mulder home. With Scully's car, Barry is in Virginia on Route 229 until he gets pulled over by the Highway Patrol for speeding. The officer notices blood on Barry's hands and the hospital bracelet on his wrist, and orders Barry out of the car. Barry refuses, and when the highwayman gets distracted by sounds he hears Scully making from inside the trunk of the car, Barry shoots and kill him. At headquarters, Mulder listens to the recording of himself conversing with Duane Barry in the travel agency. With Krycek's help, he rewinds to the part where Barry said, "Ascend to the stars." Using a phone book, he realizes Barry is heading to Skyland Mountain, which has an ad featuring this exact phrase. Without Mulder's knowledge, while requisitioning a car, Krycek makes a call to the Smoking Man, who presumably orders him to keep Mulder from catching up to Duane and Scully.
During the drive, Krycek makes comments regarding Mulder's fatigued state of mind, particularly after they drift into oncoming traffic and nearly hit a tractor-trailer. Mulder insists on continuing. At Skyland, the tram operator informs them that Duane came and went about forty-five minutes previously, and the driving journey to the summit takes about an hour. Mulder forcibly commandeers the tram, which has only just had its cables replaced and has not been tested for safety. Leaving Krycek behind, Mulder pushes the tram far above the recommended speed, only slowing down when passing the cable support towers. Just as he nears the summit, Krycek pulls his gun and beats the tram operator unconscious, before turning the tram motor off. Confused by the lack of response over the radio, Mulder climbs onto the tram's roof and attempts to climb up to the cable. Seeing this, Krycek decides to turn the tram back on, though Mulder nearly falls from the tram in the process.
At the summit, Mulder discovers Scully's car, which is empty but has blood all over the steering wheel. Searching the trunk, he finds her cross necklace, which also has blood on it. A blinding light appears through the trees and Mulder runs toward it into a clearing, where he finds a jubilant Duane. When Mulder demands to know where Scully is, Duane only responds, "They took her!" As Mulder handcuffs Duane, the blinding light appears again, causing Duane to panic until Mulder realizes it's the spotlight of an approaching helicopter.
As Duane and Mulder are patched up in a Skyland Mountain building, Mulder aggressively questions Duane, not wanting to believe that "they" have actually abducted Scully, and repeatedly asks Duane if he killed her. Duane insists that he made a deal: give them Scully and they would spare him from being abducted again. He then sees Krycek through the window with two other men (one of whom appears to be a young Bill Mulder) and freaks out. Mulder, in restraining him, does not see the men. He does see blood and some of Scully's hairs on Duane's hospital wristband, which sends him into a rage; he gets Duane by the throat and chokes him before coming to his senses. As he leaves, Duane apologizes and hopes they "aren't hurting her too much with the tests."
Outside the room, Mulder talks with Krycek, who he is suspicious of and orders not to let anyone in to see Duane. Approaching the window and seeing a bright light reflected in it, Mulder imagines some of the possible tests "they" might be performing on Scully. When he returns to the room, he is surprised to see Krycek talking to Duane and pulls him out of there. Krycek insists that Duane was gagging and he went in to help him. Their argument is cut off by the arrival of Skinner, who wants to question Duane. This is interrupted by Duane suddenly going into convulsions and dying for no apparent reason.
Back at FBI headquarters, Mulder attempts to question the doctor who performed Barry's autopsy. She refuses to provide details since it was performed by the military instead of the FBI, claiming no other doctors were available. Skinner notes that since there are no obvious causes of death, the only logical one is asphyxiation related to Mulder's choking him only minutes before. Mulder suggests that Barry was poisoned and that the toxicological tests made during the autopsy were covered up. Mulder and Krycek are both ordered to take polygraph tests.
Krycek meets with the Smoking Man, and suggests that they kill Mulder. However, the Smoking Man orders that Mulder be left alive, unless they want to risk "turning one man's religion into a crusade." A desperate Mulder tries to visit Senator Matheson, a patron of his work, only to be discouraged from doing so by his secretive informant, X . In his car, Mulder finds spent cigarettes from the Smoking Man's meeting with Krycek. Realizing Krycek's role in Scully's abduction, Mulder submits a report to Skinner accusing Krycek of impeding his investigation and killing Barry. Skinner summons Krycek to his office, only to learn that he has disappeared. Skinner then announces to Mulder that he is officially re-opening the X-Files.
Mulder meets with Margaret Scully in a park, and tries to give her Scully's necklace. Margaret returns the necklace to Mulder, asking that he give it to Scully when he finds her. Margaret also says that she had the dream again about losing her daughter; Mulder takes this as a hopeful sign that Scully may still be alive. A mournful Mulder later returns to Skyland Mountain, to the field where Scully was abducted. Seemingly alone without her, he looks up into the stars.
- David Duchovny performed his own stunts in the aerial tram sequence.
- The song playing while Duane Barry is driving through Virginia, and is pulled over by a cop, is "Red Right Hand" by Nick Cave and the Bad Seeds.
- In the tile sequence, the words "THE TRUTH IS OUT THERE" are replaced with "DENY EVERYTHING".
- The closing credits incorrectly list William B. Davis (the Cigarette Smoking Man) as "William B. David".
Cast and CharactersEdit
- Peter Lapres (Video Technician) previously played Harry Linhart in The X-Files episode "Born Again".
- Steve Railsback as Duane Barry
- Mitch Pileggi as Assistant Director Walter Skinner
- Nicholas Lea as Alex Krycek
- Sheila Larken as Margaret Scully
- Steven Williams as X