Colonel Calvin Henderson is alerted by the U.S. Space Surveillance Center that radar tracked an unidentified object as it fell from orbit and crashed in Townsend, Wisconsin. Mulder learns from Deep Throat that Henderson is the premiere reclamations expert for the Air Force. During the Cold War, Henderson was assigned to prevent technology from downed U.S. aircraft from falling into Soviet hands. Now, he is head of a crash retrieval team.

The government officially labels the crash site a quarantined area, attributing it to a toxic chemical spill. Mulder sneaks past the military units guarding the area and photographs the wreckage. His presence is soon discovered and Henderson has him arrested.

Mulder is placed in Scully's custody. She warns that when McGrath learned that he infiltrated the crash site without prior approval, he recommended that a hearing be held to discontinued the X-Files project altogether. With the hearing only a day away, Mulder insists he be given the chance to prove a UFO had crashed in Townsend.

While held in custody, Mulder meets another would-be spy, Max Fenig, a member of an organization that tracks UFO sightings. He acknowledges that he knows all about Mulder, Scully and the X-Files project, having accessed files through the Freedom of Information Act.

Max's recreational vehicle is a surveillance operation on wheels. He plays for Mulder and Scully a recording he intercepted moments after the UFO crash, in which Deputy Sheriff Jason Wright, who was the first person to arrive at the crash scene and was killed in the aftermath, radioed for fire crews. When the agents approach Mrs. Wright for information, she refuses to talk.

Dr. Jeffrey Oppenheim, who examined Deputy Wright, agrees to be interviewed. He examined the bodies of Wright and the firemen, who were also killed in the moments after the crash, all of whom died from severe burns the likes of which he had never seen before. Suddenly, the bodies of several soldiers are rushed through the hospital's corridors, each exhibiting the same burns described only moments earlier by Oppenheim. Shorthanded, Oppenheim enlists Scully's medical expertise.

Mulder aids Max when he suffers a seizure. Max blames the episode on epilepsy, but Mulder notices a diamond-shaped scar behind Max's ear which Mulder links to UFO abductions.

Before Scully has a chance to examine Max, he disappears from his vehicle. The agents track him to a warehouse, where they discover Henderson and his men surrounding the building. Before Mulder can save Max, he disappears in a blinding blue light, the presumable victim of an alien abduction.

At the hearing, Mulder defends his action as unorthodox, but necessary, given that the toxic spill was a government cover-up. McGrath's decision to fire Mulder and terminate the X-Files project is overruled by Deep Throat. He tells McGrath he likes to keep his friends close and his enemies closer.