A mental patient, identified as Duane Barry, escaped from the Davis Correctional Treatment Center, in Marion, Virginia, taking with him a hostage, Dr. Del Hakkie. At a Richmond, Virginia travel agency office, the suspect took three additional people hostage. Bureau negotiators and SWAT Team members were on the scene. Agt. Mulder was called in to aid negotiations due to the peculiar nature of the suspect’s demands. Agt. Krycek accompanied Agt.Mulder to the scene.

The agent in charge, Agt.Lucy Kazdin, briefed Agt. Mulder on the situation and the demands being made by Barry. Agt. Mulder established a phone link to Barry, and attempted to gain the release of the hostages. Barry was adamant in his refusal to grant any concessions. Barry, who claimed to be an UFO abductee, demanded to be allowed to take Dr. Hakkie to where Barry had been abducted in order to prove his sanity.

Agt. Mulder tried to calm and reassure the suspect via phone. Barry remained unmoved by Agt. Mulder’s pleas. As they talked, it became apparent that Barry was familiar with Bureau negotiation procedures. Agt. Mulder phoned Agt. Scully at her office for background on Barry. Mulder had learned that Duane Barry was a former Bureau agent who was wounded during a stakeout, and was subsequently terminated by the Bureau.

As Agt. Mulder was talking to Agt.Scully, the electrical power in the neighborhood went off unexpectedly. None of the negotiators or SWAT personnel were responsible for the outage, which caused Barry to begin firing indiscriminately.

Agt. Mulder reestablished communication with the suspect, who informed the agent that a doctor was needed. Agt. Mulder volunteered to negotiate with the suspect directly. In order to maintain a channel of support to Agt. Mulder, he was fitted by Bureau surveillance experts with an intra-audio mid-aural ear implant that would surreptitiously relay his conversations with Barry to the hostage negotiators, and simultaneously allow the negotiators to speak to Agt. Mulder.

Agt. Mulder and Agt. Janus, a trained paramedic, entered the travel office to treat the wounded hostage, a male victim suffering from an abdominal gunshot wound. While Agt. Janus treated the victim, Agt. Mulder attempted to establish a conversation with Duane Barry. Agt. Mulder managed to win the wounded hostage’s release, in exchange for himself becoming a hostage.

As Agt. Mulder was being held hostage, Agt. Scully phoned the command center with information on Duane Barry. She spoke with Agt. Krycek, telling him that Barry was not who Agt. Mulder thought he was.

When she learned that Agt. Mulder was taken hostage, Agt. Scully flew to the scene to inform the negotiators about the suspect. When Barry was shot in the line of duty, the bullet pierced Barry’s bilateral frontal lobes, destroying the moral center of his brain. Referring to a famous case that occurred a hundred years previous, Agt. Scully described the injury as causing the victim to become a pathological liar, suffering from severe delusions. Behavior became bizarre and violent, with a tendency to act out his fantasies.

Using the transmitter connected to Agt. Mulder, Scully spoke with the agent, informing him what she had learned about Barry’s condition. Unable to reply, Agt. Mulder continued his conversation with Barry. Eventually, Agt. Mulder convinced Barry to release the two women hostages, who left the premises unharmed. As he attempted to reason with Barry, Agt. Mulder was assaulted by the suspect, causing his listening device to be dislodged from his ear. Agt. Mulder, now out of communication with the command center negotiators, told Barry that when he let the women go, he forgot to lock the front door. Barry crossed to the door, putting himself in the line of fire. A sharpshooter fired one shot, striking Barry in the chest, dropping him. Agt. Mulder was not injured.

At Jefferson Memorial Hospital in Richmond, Agt. Mulder and Agt. Kazdin met to discuss the suspect, who was in critical condition. Agt. Kazdin informed Agt. Mulder that during the examination, surgeons found several pieces of metal in Barry’s gums, sinus cavity and abdomen. This information seemed to parallel Barry's claims that during his abduction by "aliens," items had been implanted in his body, and his teeth had been drilled. Further, Agt. Kazdin said that a dentist who had examined Barry’s teeth said that the holes could not have been made with current equipment without chipping or damaging the teeth.

Agt. Scully obtained one of the pieces of implanted metal from Duane Barry’s body, and took it to the Bureau’s forensic lab for analysis. When examined by a technician, small, apparently coded markings could be seen on the metal.

Later, at a supermarket, Agt. Scully took the vial containing the metallic sample and ran it across the laser scanner. Immediately the cash register’s digital display began registering a series of numbers and symbols, startling Agt. Scully and the checker. She left the store immediately, returned home, and telephoned Agt. Mulder to report the strange occurrence. As she was speaking to Agt. Mulder’s message machine, Duane Barry, who had escaped from confinement in the hospital, broke into Agt. Scully’s apartment through a window and attacked her.

Once Agt. Mulder retrieved the phone message from Agt. Scully, he went to her apartment to survey the scene. Agt. Scully’s mother, Margaret, was present, as was Agt. Krycek. No trace of Agt. Scully was found, though signs of a struggle, and blood were found in the apartment.

A meeting was convened by A. D. Skinner, with Agts. Mulder, Krycek and several unidentified senior agents present. A. D. Skinner asked for and received an update on the case from Agts. Mulder and Krycek. Agt. Mulder was asked about Barry’s mental state, and where he might have taken Agt. Scully. Agt. Mulder noted that Barry spoke of a mountain he wanted to go to, but Agt. Mulder was not aware of the location. A. D. Skinner, noting Agt. Mulder’s closeness to the case and the agent’s lack of sleep, took him off assignment and sent him home, over Agt. Mulder’s protestations.

The following day, Agt. Mulder was summoned to Bureau Headquarters’ video production unit where a video of a police stop was played, showing the killing of a patrolman. The video was shot by the patrol car’s stationary camera, and revealed the suspect, identified as Duane Barry, opening the car’s trunk following the shooting. Inside the trunk, Agt. Scully could be seen, bound and gagged.

Agt. Mulder reviewed audio tapes of the Barry hostage situation, where Barry stated that he wanted to "go to the mountain, ascending to the stars." Noting that the patrolman was killed in Rixeyville, Virginia, on Route 229, which leads to the Blue Ridge Parkway, Agt. Mulder consulted a Virginia Yellow Pages directory, where he found a display ad for Skyland Mountain, with the legend, "Ascend to the Stars." Determining that Skyland must be the destination sought by Barry, Agt. Mulder told Agt. Krycek to get his car and to meet him in the garage. Krycek hesitated, wondering what Agt. Mulder intended to do about A. D. Skinner’s directive to Agt. Mulder ending his participation in the Barry case. Agt. Mulder told Agt. Krycek he would "deal with it."

In the garage, Agt. Krycek passed on the information about their destination to the Cigarette-Smoking Man before driving to pick up Agt. Mulder.

At Skyland Mountain, the agents contacted the watchman, who was shown a photo of the suspect. He identified the photo, telling the agents that Barry had driven to the summit by the back road, as the tram to the top was closed for the summer. Agt. Mulder forced the watchman to engage the tram to take him to the top, as Agt. Krycek remained in the control room with the watchman. As Agt. Mulder ascended the mountain, Agt. Krycek assaulted the watchman, striking him with his weapon. Now controlling the mechanism, Agt. Krycek brought the tram to a halt, effectively trapping Agt. Mulder. Once he had accomplished this, Agt. Krycek phoned an unknown individual and informed him that he had Agt. Mulder stalled and would hold him until the person on the phone advised a course of action.

Agt. Mulder used a trapdoor to escape the tram, and climbed to the tower ahead. Agt. Krycek, viewing Agt. Mulder’s actions via the control room’s video monitor, restarted the tram mechanism. Agt. Mulder managed to reach the tower before the tram crushed him. Reaching the top, Agt. Mulder ran to the forest summit, seeking Duane Barry and his hostage. Discovering Agt. Scully’s abandoned car, Agt. Mulder checked the trunk but found only Agt. Scully’s necklace, which he retrieved. Agt. Mulder was distracted by a series of glowing lights behind the trees surrounding him as a humming noise filled the air. As he moved toward the treeline, the lights were extinguished and the whine of an aircraft engine replaced the hum. A black helicopter swooped overhead, then disappeared. Hearing laughter, Agt. Mulder proceeded to a clearing, where he found Duane Barry, laughing and shouting. Agt. Mulder pointed his weapon at Barry, ordering the man to lie down on the ground. After a moment the suspect complied. Agt. Mulder removed a weapon from the man’s waistband and asked Barry about Agt. Scully’s location, at which time the suspect told Agt. Mulder that "they" had taken her and left him behind.

At the Skyland Grill, Duane Barry was tended to by paramedics as Agt. Mulder was questioning him. Barry stated again that "they had taken her...that was the deal. Her instead of me." Agt. Mulder asked Barry if he had killed Agt. Scully. The suspect replied in the negative.

As he was being questioned, Duane Barry noticed two men in dark suits watching the interrogation. He told Agt. Mulder that the men had seen the abduction, that they were connected with the military, and were "in on it." Agt. Mulder lost control of the situation and slammed Barry into a wall.

Agt. Mulder left the suspect alone in the room, telling Agt. Krycek to let no one in, that he alone would interrogate Barry. Soon afterward Agt. Mulder caught sight of Agt. Krycek interviewing the suspect. Agt. Mulder signaled to Agt. Krycek, who left the room. Agt. Mulder questioned Agt. Krycek’s actions disregarding his orders. Agt. Krycek said that he heard Barry gagging, and went to his aid. He told Agt. Mulder that Barry told him he had been choked by Agt. Mulder.

At that moment, A. D. Skinner arrived with three Bureau agents from the Violent Crimes Section. As A. D. Skinner questioned Agt. Mulder as to why he had disobeyed a direct order, a deputy called for paramedics to come to Barry’s aid. Entering the office, the agents found Barry on the floor, his face blue. Paramedics attempted resuscitation, but were unsuccessful. The suspect expired at the scene.

Later, in A. D. Skinner’s office, the case was reviewed by A. D. Skinner and the Cigarette-Smoking Man, with Agt. Mulder and a senior agent present. Agt. Mulder denied choking Barry, even though A. D. Skinner’s reading of the autopsy report revealed that the likely cause of death was prolonged hypoxemia, secondary to asphyxiation, as the victim exhibited contusions and a bruised larynx.

Asked to respond, Agt. Mulder stated he had interrogated Barry about Agt. Scully’s disappearance, and was pushing the suspect because he was uncooperative. He admitted losing control momentarily, but asserted that Barry was alive when he left the room. Agt. Mulder affirmed that Agt. Krycek spoke to Barry after Agt. Mulder had left the room.

A. D. Skinner informed Agts. Mulder and Krycek that the OPC requested that each agent take a lie detector test to ascertain the veracity of their statements. Agt. Mulder asserted that there was a possibility that Barry was killed by poisoning, either by ingestion or injection, but that evidence of lethal administration was unavailable, as the pathologist’s report was incomplete. Agt. Mulder further charged that the military had covered up the toxicological findings, because they knew where Agt. Scully was. Agt. Mulder left the office at this point.

At headquarters, Agt. Mulder confronted Agt. Krycek near the office of professional responsibility (OPC) and requested that Krycek turn over his car keys to Agt. Mulder. Agt. Krycek complied.

In an attempt to see Senator Richard Matheson in the Senate Office Building, Agt. Mulder was intercepted by his confidential contact, X, who told him that the Senator could do nothing for him at that time. Agt. Mulder attempted to question X, but could get no information. Returning to Agt. Krycek’s car, Agt. Mulder pondered his options. As he sat in the car, he noted cigarette butts in the ashtray, and remembering that Agt. Krycek did not smoke, examined the remains of the cigarettes, realizing to whom they belonged.

Returning to A. D. Skinner’s office, Agt. Mulder produced the cigarette butts along with a typed report that claimed that Agt. Krycek was suborned by an outside agency to impede a federal investigation, and might also be guilty of killing a suspect in a capital murder case. The report further alleged that Agt. Krycek might be responsible for the murder of the watchman at Skyland Mountain. Agt. Mulder said he believed that Krycek gave away Agt. Barry’s and Agt. Scully’s whereabouts to whomever he was working for, most likely a covert arm of the military.

A. D. Skinner attempted to contact Agt. Krycek, but was informed that the agent didn’t report from work that morning, and that his home number had been disconnected.

Stymied in his attempts to get the truth, A. D. Skinner informed Agt. Mulder that as of that moment, the X-Files were being reopened, on his authority.

Later, Agt. Mulder visited Agt. Scully's mother, and offered her Agt. Scully's gold cross and necklace, which he had found in Duane Barry's car at Skyland Mountain. Mrs. Scully requested that Agt. Mulder keep the cross, and give it to Agt. Scully when he found her.