Four years after his abduction, Max Fenig (Scott Bellis) is traveling on Flight 549, which is flying over upstate New York. He watches another man on the plane who seems to be following him. The man heads to the plane's bathroom, where he assembles a zip gun. However, when he comes back out, the airplane begins shaking and a bright light flashes outside, showing that the plane is encountering a UFO. The emergency door next to Max's seat is opened.
Elsewhere, Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) celebrate Scully's birthday. They are approached by a woman named Sharon Graffia, who claims to be Max's sister; she tells them that Max planned to deliver something to Mulder, but that his flight to Washington has crashed. The agents head to the crash site in Northville, New York, and attend an NTSB meeting where Flight 549's final transmissions are shown. Mulder theorizes that the plane was forced down by aliens attempting to abduct Max; the NTSB team, led by chief investigator Mike Millar (Joe Spano), dismisses his claims.
When Mulder and Scully survey the crash site, they realize that there is a nine-minute disparity between the crash and the time on the victims' wristwatches, indicating missing time. Mulder believes that Max was abducted from the plane and that his body will not be found. Meanwhile, Scott Garrett, a Man in Black posing as an NTSB investigator, steals the zip gun from the assassin's body and erases his face and fingerprints with acid. Larold Rehbun, a passenger who sat next to Max, is found alive. His injuries indicate exposure to radiation.
Upon being confronted by Scully, Sharon denies that Max brought a radioactive substance aboard the plane, but divulges that she is not actually Max's sister. She also gives up details about his underground life. Scully subsequently tells Mulder that Max worked at a nuclear weapons assembly facility in Colorado under an alias, and believes that he may have caused the crash after bringing plutonium on board; Mulder, however, believes that Max was taken off the plane by a UFO, and that Rehbun's injuries were caused by exposure to the craft. Scully informs Mulder that Max's body has already been pulled from the crash site. Meanwhile, Sharon is abducted from her hotel room.
After identifying Max's body, Mulder finds that the wristwatches have been stolen from the other victims. He refutes the NTSB's official explanation of malfunction as a cause of the crash, and is doubtful that the true cause will be found unless they discern what happened during the nine minutes of missing time. The agents visit Sergeant Louis Frish (Tom O'Brien), an air traffic controller from the U.S. Air Force who was on duty during the crash. Frish denies anything unusual happened. However, after the agents leave, Frish and a colleague argue over whether to reveal the "truth" about Flight 549's demise.
After finding Sharon's trashed hotel room, Mulder meets with Millar, who tells him that the door was pulled off the plane from the outside while it was in flight. Later, Frish finds his colleague dead from a faked suicide. A group of commandos arrive to capture Frish, but he escapes. Frish goes to see Mulder and Scully, telling them that he lied before and that his commanding officer had ordered him to track the plane's coordinates as it was being intercepted by a second aircraft. Seconds later, there was an explosion and the plane disappeared from his radar. Mulder believes that a third aircraft, a UFO, approached the plane and was destroyed by the second aircraft, also causing the Flight 549 crash. The agents leave with Frish and are soon chased by the commandos but they manage to lose them by driving under a landing plane. Meanwhile, Millar returns to the crash site and encounters a UFO. He finds Sharon nearby, having just been returned by her abductors.
Scully returns to Washington with Frish while Mulder heads to Great Sacandaga Lake, searching for the crashed UFO. Scully brings Frish to a local bar where they run into fellow FBI agent Pendrell (Brendan Beiser). The Man in Black soon enters the bar seeking to kill Frish, accidentally shooting Pendrell instead while Scully shoots him back. Meanwhile, Mulder arrives at the lake where he finds a team of men already searching for the crashed UFO. He dives underwater and finds the craft, including an alien body. Before he can return to the surface, a bright light shines down from above the water.