Mulder and Scully investigate a UFO sighting in Reagan, Tennessee. They interview a truck driver named Ranheim, who claims he fired his shotgun at a mysterious object in the sky. Ranheim, however, changes the details of his story, prompting Mulder to speculate that he has something to hide. The agents also realize that Ranheim exhibits symptoms of Gulf War Syndrome, an illness that normally afflicts veterans of the conflict in Iraq. Ranheim claims he is not a veteran of that war.

After further investigation, Scully discovers that Ranheim's real name is Frank Druce, a former Special Operations officer in Iraq who had been admitted to VA hospitals for treatment of his illness. Meanwhile, Mulder receives top secret information from Deep Throat that Druce was transporting the wreckage of a UFO that was shot down over Iraqi air space. But other evidence hints that the truck is a decoy, and that the real wreckage is actually being kept at Fort Benning in Georgia. Mulder and Scully realize that Deep Throat has been deliberately leaking them misinformation.

When Mulder confronts Deep Throat, he admits that he tried to lead the investigation away from the truck. He justifies his action by stating that the country is not ready to comprehend a closely guarded government secret. He also confirms that the agents are under constant surveillance.

Determined to uncover the truth, Mulder and Scully resume their search for the truck. Their diligence pays off, and the vehicle is located on a remote roadway. While surveying the truck from afar, the agents' vehicle is suddenly engulfed by an intense light. The truck comes to a stop and the agents open its doors. Inside, they find evidence that suggests an Extraterrestrial Biological Entity, or E.B.E., had been inside.

Mulder and Scully suspect that the E.B.E. had been shuttled to a top secret government facility where a host of UFO sightings had been reported in the previous week. With the aid of an extreme government watchdog group called "The Lone Gunman," the agents gain access to the heavily-guarded facility. The agents' presence is detected and they are taken into custody, but not before Mulder comes close to seeing the E.B.E.

Deep Throat comes to Mulder's aid. He reveals that after the Roswell UFO incident in 1947, the most powerful governments in the world signed a top secret treaty ordering the execution of any E.B.E. that might survive a UFO crash. Deep Throat reveals that he carried out the murder of the E.B.E., and to atone for his act, he will continue to leak Mulder top secret information. Mulder is released, but he remains unsure that Deep Throat is telling the truth.