Mulder and Scully investigate the strange disappearance of Lieutenant Colonel Robert Budahas, a test pilot for the military who experienced a psychotic episode and was supposedly hospitalised for treatment. Mulder suspects that Budahas may have met the same fate as six other pilots who mysteriously vanished from Ellens Air Base while participating in experimental aircraft test flights. Mulder hints to Scully that the disappearance may be linked to the paranormal-classifying it as an "X-File" case.
Mulder is approached by a mysterious man, dubbed "Deep Throat", advises that the investigation be dropped.
But Mulder and Scully ignore the advice and interview Mrs Budahas, who describes her husband's unpredictable behaviour, strange skin rash and aversion to discussing this work on the military's top-secret projects.
The agents theorize the pilots may have been associated with Project Aurora, a code name given the Pentagon's secret testing of sub-orbital spy craft. Aided by tips from reporter Paul Mossinger and UFO buff Ladonna, the agents stake out a fenced area near the base. That night, Mulder and Scully watch in amazement as two brightly lit objects shoot through the night sky manoeuvring at incredibly speed.
The agents give chase when two teenagers, Emil and Zoe, are spotted climbing through a hole from the opposite side of the fence. But the hunters become the hunted when a helicopter from the base bears down on the group. The foursome escape, retreating to a restaurant where Zoe and Emil recount tales of watching the light show.
Mulder tells a disbelieving Scully that the military may be flying planes built using technology from a UFO.
Mrs Budahas phones the agents at their hotel when her husband suddenly reappears. But the Lieutenant Colonel cannot remember any details having to do with his past and the military.
Mulder tells Scully he believes Budahas' memory has somehow been drained, and that he, like the other missing pilots who tested the mysterious aircraft, are physiologically incapable of dealing with the stress created during the flights. The agents are approached by men who seize their evidence and order them to leave town. But Mulder returns to the base, and using Emil and Zoe as guides, climbs through the hole in the fence. Alone on the base, Mulder is spotted by a UFO and taken prisoner by base security that suddenly arrives. He is then sedated and treated by mysterious figures acting as doctors. Scully is attacked by Mossinger, who she discovers has been working for the military all along. Scully overpowers him, taking him hostage at gunpoint. She uses Mossinger to find Mulder and when she learns he is in custody of the military trades Mossinger in return for Mulder. But when he is returned to her, he is unable to recall his encounter with the UFO or what happened while he was on the base because of the treatment they gave him.
Back in Washington, Deep Throat once again approaches Mulder while jogging. Deep Throat warns Mulder that the agents have chosen a very dangerous path and their lives are in danger now that they know the truth about the existence of extraterrestrial life.
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