At the Headless Woman's Pub, waiters singing "Happy Birthday" approach Mulder and Scully's table. Scully is surprised that her partner remembered the occasion. Before the celebration continues, the agents are approached by Sharon Graffia, who identifies herself as the sister of Max Fenig (the alien abductee seen in "Fallen Angel"). Fenig was killed in an airplane crash in Upstate New York two hours earlier. It was Fenig's wish that the agents be sought out should any harm befall him.

     The agents attend a Go-Team meeting assembled by the National Transportation Safety Board. Mike Millar, the man in charge of the operation, plays a tape recording of the last radio exchange between Flight 549 and air traffic control in Albany. During the recording, the pilot makes reference to an "intercept." Mulder believes is an indication the airliner was forced out of the sky. But his comments before the group are met with great skepticism.

     The agents comb the crash site for possible clues. Mulder realizes there is a nine minute discrepancy between the official time of the crash and the time indicated on passengers' wrist watches. In the distance, an investigator named Garrett sprays an acid-like substance on one of the bodies, dissolving the victim's fingertips and face. A few moments later, other Go-Team members pull a survivor, Larold Rebhun, from the wreckage. Scully concludes he was exposed to extreme radiation. Mulder tells Scully that he believes Fenig was abducted from the aircraft by being sucked out of the emergency exit door. However, Go-Team members find Fenig's body amongst the debris field.

     The agents interview Louis Frish, who, along with Armando Gonzales, manned the Air Force Reserve air control tower on the night of the crash. Louis claims there was no radio contact between the Air Force and the civilian plane. Later, Louis finds Gonzales' dead body inside the control tower. Several government men storm the tower. Louis avoids capture by hiding on the roof. Later, Sharon Graffia disappears from her motel room. Mulder concludes she was abducted by a UFO.

     Louis Frish tells Mulder, Scully, and Millar that he-not an air traffic controller in Albany-was the last person to communicate with Flight 549. Louis explains that his commanding officer ordered him (along with Gonzales) to lie to investigators. The men saw an unidentified radar blip enter Flight 549's airspace. Moments later, there was an explosion. Mulder speculates that a third, unidentified aircraft shot down the intercept craft-but is at a loss to explain the absence of a second crash site. As the agents drive Louis away from the Go-Team's headquarters, two automobiles give chase. In an attempt to outmaneuver his pursuers, Mulder drives onto a runway. An airliner lands on the strip, narrowly missing Mulder's car. The two chase cars break off their pursuit. Later, Mike Millar encounters a UFO hovering above the crash site. He finds Sharon Graffia nearby.

     Scully and Louis await a Federal Marshal at the Headless Woman's Pub. Garrett enters with a gun. Scully draws her weapon and a shoot-out ensues. Agent Pendrell, who happened to be frequenting the bar, is shot in the chest. Scully manages to shoot Garrett in the leg.