While Agts. Mulder and Scully were celebrating Agt. Scully’s birthday at the Headless Woman Pub in Washington, D.C., they were approached by a woman who identified herself as Sharon Graffia. Graffia claimed to be the sister of Max Fenig, known to Agts. Mulder and Scully from their work on Case 1X09 (Code Name: Fallen Angel). Graffia revealed that earlier that night, the plane in which Fenig had been traveling had crashed. She further stated that Fenig had been in the possession of something that he had claimed the government would kill to possess. According to Graffia, Fenig had instructed her to contact Agt. Mulder if he failed to arrive on schedule.

Agts. Mulder and Scully immediately traveled to New York State to attend a meeting of a team of National Transportation Safety Board (NTSB) investigators assigned to determine the cause of the crash of the flight in which Fenig had died. The meeting was presided over by team leader Mike Millar. At that meeting, the Agts. Mulder and Scully learned that the flight, designated 549, had lost radio contact at 1900 hours that night and had then crashed into a wooded area approximately thirty miles from Albany, New York. None of the 130 passengers had yet been found alive. During the meeting, Millar played the tape of the last radio exchange between air traffic control and the pilot of Flight 549. The pilot had announced an intercept and called for help before ceasing to respond to the controllers’ transmissions. Agt. Mulder informed the investigators of Fenig’s presence on the plane. He described Fenig as a repeat alien abductee who had predicted the crash. Millar and the team expressed skepticism as to the existence of alien life forms. Millar also pointed out that Fenig’s name did not appear on the flight’s passenger manifest. Millar stated that as Agt. Mulder’s questions did not arise from an official Bureau position, Agt. Mulder was trivializing the investigation.

Early the next morning, Agts. Mulder and Scully joined the investigators at the crash site. Agt. Scully learned that the investigators were attributing the crash to weather phenomena. Agt. Mulder suggested that the crash had been deliberately caused as a means of killing Fenig. Meanwhile, unbeknownst to Agts. Mulder and Scully, two investigators, one of them identified as Garrett, located a plastic handgun on the body of a passenger. Garrett and the other investigator removed the gun and his watch, and sprayed the gunman’s fingers and face with a substance that obliterated his fingerprints and facial features.

Agts. Mulder and Scully meanwhile retrieved two watches from the wreckage. Despite the reported time of the crash, 7:52, both watches read 8:01, a nine-minute discrepancy. Agt. Mulder expressed his doubt that Max Fenig had remained on the flight until the end. An investigator then discovered a passenger alive. Examining the passenger, Agt. Scully called for a burn unit, oxygen, and intravenous saline.

That night, at a small local airport, Sharon Graffia delivered to Agt. Scully a collection of Max Fenig’s letters. Agt. Scully asked Graffia what Fenig had been carrying on the flight. She told Graffia that the burned passenger’s injuries had been caused by highly radioactive material. Graffia claimed to have no further information. After reading Fenig’s correspondence, Agt. Scully met Agt. Mulder in an airport hangar where pieces of wreckage had been collected. Agt. Mulder speculated that Fenig had been seated in seat 13F, using the alias Paul Gidney, which Agt. Scully recognized from Fenig’s correspondence. Based on her reading of that correspondence, Agt. Scully suggested that Fenig had been carrying plutonium, which had been exposed during the flight and caused the crash. Agt. Mulder predicted that the facts would support the conclusion that Fenig had been abducted from the plane by alien life forms but that that conclusion would nevertheless be dismissed. Agt. Scully countered by informing Agt. Mulder that Fenig’s body had in fact been found, with radiation burns similar to those of the other burned passengers. In a hangar where the bodies had been bagged, Agt. Mulder made a positive identification of Fenig. He also discovered his own business card in Fenig’s possession. Agt. Mulder then checked other body bags and noted that none of the bodies wore a watch. Agt. Scully reported to Sgt. Mulder the investigators’ most recent conclusion that the crash could not be attributed to radiation and remained unexplained. Agt. Mulder expressed his belief that nine minutes had somehow disappeared from those on the plane at some point during the flight.

Meanwhile, at the Paradise Motel, in Northville, New York, Sharon Graffia reviewed Fenig's letters. The room began to shake. A blinding white light appeared in the windows, followed by a high wind.

The next morning, Agts. Mulder and Scully proceeded to the control tower at Von Drehle Air Force Reserve Installation. There, they interviewed air traffic controller Sergeant Louis Frish. Sgt. Frish reported that the NTSB team had interviewed him on the night of the crash. He further stated that he and another air traffic controller identified as Sergeant Gonzales had observed Flight 549 on the radar screen but because Flight 549 was a commercial flight not impinging on military air space, they had had no reason to contact the plane. The two air traffic controllers had seen Flight 549 drop rapidly and crash. They had reported that observation to air traffic control in Albany. After interviewing Sgt. Frish, Agts. Mulder and Scully noted that the initial report had stated no radar confirmation of the plane’s crash. After the agents left the tower, Sgt. Gonzales approached Sgt. Frish. Sgt. Gonzales insisted that, if questioned by the agents, Sgt. Gonzales would no longer lie about the events of the crash. Sgt. Frish expressed anger and drove away.

Agts. Mulder and Scully then proceeded to the Paradise Motel, where police had arrived in response to a call from the motel manager. The manager claimed that Sharon Graffia appeared to have wrecked the room the agents had rented for her and had then left the motel. The agents discovered the motel-room door bent and removed from its jams. Max Fenig’s papers were strewn about the room. Agt. Mulder suggested that Graffia had been abducted. Mike Millar then arrived at the motel and informed the agents that he had discovered something inexplicable in the Flight 549 wreckage. In Agt. Mulder’s motel room, Millar showed the agents a transparency that revealed cracks on the exit door of the downed plane, which Millar described as having been blown not inward but outward. Millar described such an event as impossible during normal operation.

That night, in the control tower at Von Drehle Air Force Reserve Installation, Sgt. Frish, approaching Sgt. Gonzales in order to apologize for his earlier outburst, found Sgt. Gonzales shot dead, still holding a gun in his hand. Observing cars driving toward the tower, Sgt. Frish fled. Armed men in military attire rushed into the tower, commanded by Garrett. They failed to locate Sgt. Frish, who concealed himself on the top of the tower.

In his motel room, Agt. Mulder listened to the last radio transmission of Flight 549. He identified the voice of the air traffic controller on the tape as that of Sgt. Frish. Agt. Mulder then summoned Agt. Scully to his room. As Agt. Scully proceeded to Agt. Mulder’s room, she was accosted by Sgt. Frish. Frish then confessed to Agt. Scully that he had caused the crash.

Agt. Mulder, Agt. Scully, and Sgt. Frish proceeded to the hangar where Mike Millar was continuing the investigation. Millar stated his belief that the air traffic controller on the tape was an Albany-based civilian. Sgt. Frish contradicted Millar, stating that he and Sgt. Gonzales had been ordered to give coordinates to Flight 549 at fifteen-second intervals. Sgt. Frish and Sgt. Gonzales had observed a second air craft enter Flight 549’s air space and shadow Flight 549. They had then observed an explosion and the downing of Flight 549. Agt. Mulder suggested that a third aircraft, undetected by radar, had intercepted Flight 549 and been shot down by the second aircraft, in turn causing the downing of Flight 549. According to Agt. Mulder, the unseen craft would also have crashed, in a location known only to the military. Because the military was eager to destroy evidence of that crash, Agt. Mulder said, Sgt. Frish was now in danger. Millar suggested that they search for a second crash site. As Agts. Mulder and Scully drove with Sgt. Frish across the tarmac, they were pursued by two vehicles. Agt. Mulder drove rapidly onto a runway, encountering a landing plane. Coached by Sgt. Frish, Agt. Mulder drove under the plane at high speed, narrowly escaping collision. The pursuing vehicles were forced by the plane off the runway, where they stopped.

Meanwhile Millar sighted a UFO shining a bright searchlight on the ground. The craft then appeared to vanish. Moments later, a bright white light blinded Millar. Millar then encountered Sharon Graffia. Graffia, distraught, begged Millar not to let "them" take her again.

At the Fulton County Airport, Agts. Mulder and Scully, accompanied by Sgt. Frish, chartered a plane. Agt. Mulder and Sgt. Frish agreed that Great Sacandaga Lake was a logical place for the unseen second craft to have crashed. Agt. Scully and Sgt. Frish left in the charter plane, bound for Washington, D.C. Agt. Mulder drove to a residence, which belonged to a hunting and fishing guide identified as Bearfeld, near Great Sacandaga Lake. Bearfeld described to Agt. Mulder mysterious lights he had seen hovering above the lake near an area known as Democrat Point. In Bearfeld’s boat, Bearfeld and Agt. Mulder approached Democrat Point by water. Using scuba gear, Agt. Mulder dove below the surface of the lake, where he discovered unusual wreckage. In the wreckage, he found the body of what appeared to be an Extraterrestrial Biological Entity. He then observed armed frogmen swimming toward the wreckage. Agt. Mulder fled, leaving his scuba tank behind, and swam to shore. On shore, Agt. Mulder was pursued and arrested by soldiers. Agt. Mulder was then transported to the Military Police building at Von Drehle Air Force Reserve Installation, where he was detained.

Meanwhile Agt. Scully and Sgt. Frish arrived at Agt. Scully’s apartment in Washington, D.C. There, Agt. Scully assured Sgt. Frish that she would arrange federal protection for him. Sgt. Frish expressed guilt for the having caused the deaths of the passengers on Flight 549 and for having lied to federal investigators. Agt. Scully attempted to persuade Sgt. Frish that he was not to blame. After being warned by Agt. Scully not to reveal his whereabouts, Sgt. Frish made a phone call to his girlfriend.

Agt. Scully and Sgt. Frish then proceeded to the Headless Woman Pub, where Agt. Scully had arranged for Sgt. Frish to be met by United States Marshals. There, Agt. Pendrell bought drinks for Agt. Scully and Sgt. Frish. Garrett entered the bar and fired a handgun at Sgt. Frish. The bullet struck Agt. Pendrell. Agt. Scully fired her weapon at Garrett, wounding him. Agt. Scully attended to Agt. Pendrell’s lung wound, then followed Garrett into the street. She instructed police to call for Emergency Medical Technicians. Observing that Garrett had escaped, Agt. Scully returned to the bar, where she coached the EMT team and reassured Agt. Pendrell. During that process, Agt. Scully’s nasopharyngeal tumor briefly caused her nose to bleed. Sgt. Frish assured Agt. Scully that he had not revealed their whereabouts. Agt. Scully concluded that someone in the federal government had revealed that information to Garrett.

A. D. Skinner arrived at the bar and informed Agt. Scully that her order for United States Marshals' protection for Sgt. Frish had been countermanded by the Joint Chiefs of Staff. According to A. D. Skinner, both Sgt. Frish and Agt. Mulder were to be placed under military arrest. Agt. Scully protested that the military was responsible for the downing of Flight 549. A. D. Skinner informed Agt. Scully that the military now admitted that fact but had offered an explanation. Noting blood on a tissue held by Agt. Scully, A. D. Skinner reminded Agt. Scully that he was responsible for her welfare and strongly suggested that she be examined at the hospital to which she would accompany Agt. Pendrell. Later that night, Agt. Pendrell died of his gunshot wounds.

The next day, Agt. Scully traveled to the Military Police building at Von Drehle Air Force Reserve Installation to meet with Agt. Mulder and oversee his release. There, the agents discussed the military’s explanation for the crash. According to the military, inaccurate coordinates had been given to the pilot of an F-15 Eagle fighter plane, which had collided with Flight 549, causing the collision and prompting Sgt. Gonzales to commit suicide. Agt. Scully told Agt. Mulder that she had heard persuasive recordings of exchanges between air traffic control and the F-15 that tended to support the military’s version. Agt. Scully also admitted that she no longer knew what to believe. Agt. Mulder showed Agt. Scully radiation burns on his head and described the submerged wreckage he had discovered as a UFO shot down by the military. Agt. Scully argued that Mike Millar had found no evidence that Flight 549 had been involved in a collision. She added that Millar had found Sharon Graffia wandering near the crash site. She also revealed that Graffia was not Max Fenig’s sister but an unemployed aeronautical engineer with history of mental illness. She then informed Agt. Mulder of Agt. Pendrell’s death.

Seeking clues, Agts. Mulder and Scully proceeded to Max Fenig’s residence in a trailer park in Barnes Corner, New York. There, Agt. Mulder showed Agt. Scully the business card that had been in Fenig’s possession. The agents viewed a videotape in which Fenig described his abductions and a cover-up conspiracy conducted by the government, the Bureau, and the military-industrial complex in order to keep secret the recovery of advanced technology from downed alien aircraft.

At the shore of Great Sacandaga Lake, a covert military operation recovered wreckage and the bodies of Extraterrestrial Biological Entities from the water. The operation was overseen by Garrett. When an injured diver emerged from the water blistered with radiation burns. Garrett expressed satisfaction at having located what he was seeking.

Meanwhile, in the hangar at the crash site, Millar addressed his investigation team. 76% of the bodies had been recovered and identified, but 3000 man-hours of investigation had revealed no evidence that would refute the Air Force's description of events. Millar asked for wrap-up reports and commended the team on their efforts. After the meeting, Agts. Mulder and Scully spoke to Millar, who thanked them for leading the team to the facts. Agt. Mulder expressed his opinion that Millar was not satisfied with the results of the investigation. Agt. Scully informed Millar that covert actions engaged in by the military in promoting its version of events had indeed raised legitimate suspicions of a cover-up.

Agt. Mulder then related for Agt. Scully and Millar his conclusions regarding the crash. According to Agt. Mulder, Max Fenig had been followed onto the plane by a passenger assigned to take Fenig’s package, which contained physical proof of the existence of extraterrestrial intelligence. Flight 549 had then been intercepted by a UFO, which had taken control of the aircraft’s systems. Under orders from their superiors, Sgt. Frish and Sgt. Gonzales, not knowing that the UFO was locked onto Flight 549 and that time would stop on Flight 549 for nine minutes, had then given a fighter plane Flight 549’s coordinates. The UFO had meanwhile sucked away Flight 549’s emergency exit door. Fenig had been removed from Flight 549 and taken aboard the UFO. That event had had no effect on Flight 549. In Agt. Mulder’s opinion, Fenig had probably been in the process of being returned to Flight 549 when the fighter plane had shot down the UFO controlling Flight 549. Flight 549 had thus lost altitude and crashed to the ground. The UFO had crashed in Great Sacandaga Lake.

Millar then showed the agents Fenig’s knapsack, retrieved from the wreckage. He stated that the knapsack had been linked to radioactivity. In the knapsack was Fenig’s baseball cap with a logo from National Investigative Committee of Aerial Phenomenon (NICAP). Millar added that he would mention the knapsack in his report but would not refer to it as a causal factor. Privately, Agt. Scully defended Millar’s decision to Agt. Mulder. She described Agt. Mulder’s theory as a house of cards. Agt. Mulder argued that the deaths of Agt. Pendrell and Max Fenig would be rendered meaningless if the agents failed to identify the cause of the crash. He suggested that Agt. Scully interview Sharon Graffia.

Agt. Mulder returned to Max Fenig’s trailer, which he observed to have been a scene of a frantic search. The trailer park manager, Mr. Ballard, entered the trailer. Ballard gave Agt. Mulder Fenig’s mail. Agt. Mulder then re-screened the videotape of Fenig and this time noted Sharon Graffia as the camera operator. In Fenig’s mail, Agt. Mulder discovered a ticket for the luggage claim at Syracuse Hancock International Airport, addressed to Fenig from Fenig’s alias, Paul Gidney.

At the Northeast Georgetown Mental Health Center, Agt. Scully interviewed Sharon Graffia. Graffia admitted that she was not Max Fenig’s sister. Agt. Scully noted radiation blisters on Graffia’s face and suggested that as an aeronautical systems engineer, Graffia had stolen something radioactive from her employer at Fenig’s behest. Graffia described the item she had taken as alien technology consisting of three interlocking parts. She and Fenig had divided up the parts. Fenig had been carrying one part on Flight 549. Graffia had also had one part. She described both of those parts as having been confiscated.

At Syracuse Hancock International Airport, Agt. Mulder used Fenig’s claim check to retrieve a knapsack. He then noted men pursuing him. Identifying himself as a federal officer, Agt. Mulder was shown by the claim attendant to the security entrance to the terminal. Agt. Mulder then received a call from Agt. Scully. He informed her of his whereabouts and that he had retrieved Fenig’s package. Agt. Scully warned Agt. Mulder against removing the highly radioactive object from its container. Agt. Mulder placed the knapsack on the airport luggage X-ray belt and observed its image on the monitor. He noted that the object in the knapsack consisted of three circular pieces housed in a small superstructure. Agt. Scully suggested that the current case actually concerned industrial espionage. Agt. Mulder announced his intention to fly to Washington, D.C., on flight 501. He instructed Agt. Scully to arrange for transport from Dulles Airport. Agt. Mulder then boarded the plane. Unbeknownst to Agt. Mulder, Garrett was also on board.

During the flight, Garrett took a seat beside Agt. Mulder and attempted to engage him in conversation. Agt. Mulder, noticing a gunshot wound on Garrett's leg, then pointed his firearm at Garrett, while concealing it under his coat, and ordered Garrett not to move. Garrett argued that if Agt. Mulder fired and missed, the effect on the plane would be catastrophic. Garrett claimed that in that event, he would take the knapsack and escape using a parachute he had placed in a nearby overhead bin. Garrett expressed his willingness to die for his cause. Agt. Mulder asked Garrett what form of alien technology the object in the knapsack represented.

Agt. Mulder then led Garrett to the lavatory, wedging the door closed with the drinks trolley. He called Agt. Scully at Dulles Airport and informed her of the situation, asking her to call A. D. Skinner. While speaking on the phone to Agt. Scully, Agt. Mulder noted that his watch had stopped. Agt. Mulder urgently informed the flight attendant that an interception and boarding were about to occur. Garrett emerged from the lavatory carrying a plastic handgun. He ordered Agt. Mulder to put down the knapsack. Agt. Mulder complied. At that moment, the aircraft began to buck. Garrett retrieved the knapsack. Agt. Mulder warned Garrett to drop it. The emergency exit door strained outward. The turbulence subsided as blinding white light filled the cabin. Agt. Mulder pulled the trigger of his firearm. No shots were fired.

When the aircraft landed at Dulles International Airport, A. D. Skinner and Agt. Scully boarded the aircraft. Agt. Mulder informed them that Garrett and the knapsack were gone. There was a discrepancy between the actual time and the time indicated by Agt. Mulder’s watch.

In Max Fenig’s trailer some days later, Agts. Mulder and Scully met with Sharon Graffia and again viewed Fenig’s videotape. The agents returned Fenig’s records to Graffia and left the trailer. Outside, Agt. Scully pointed out that she had never even learned Agt. Pendrell’s first name. She thanked Agt. Mulder for the gift he had given her on her birthday, a key chain commemorating the landing of Apollo 11 on the moon.

The case remains open.