With the X-Files project officially disbanded, Mulder and Scully return to rank and file FBI investigations. The agents, having been exposed to extraordinary cases involving extraterrestrials and the paranormal, can hardly conceal their boredom. Believing that the agency has them under surveillance, they meet in the parking garage of the Watergate Hotel. There Mulder confesses to Scully that he has grown depressed about his mission in life-finding evidence that proves his sister was abducted by aliens years earlier. He laments that despite having numerous close encounters with UFOs, he still possesses no physical evidence that proves extraterrestrials exist. He is losing interest in finding "the truth." Mulder is later summoned to the Capitol Building by Senator Richard Matheson, an X-Files patron, who lets him in on a big secret: an abandoned radio telescope in Puerto Rico was the site of a UFO encounter.

Mulder flies to Puerto Rico immediately, hoping to beat the Blue Beret UFO Retrieval Team before they can confiscate evidence that contact was made. He makes forced entry into the facility, where he discovers a reel to reel tape spinning unattended on a tape recorder. A terrified Puerto Rican man named Jorge draws Mulder an image that seems to be extraterrestrial that he witnessed at the site.

When Mulder does not show up for work, Scully begins an investigation. She searches his apartment and discovers a piece of paper containing a "Wow Signal," a radio transmission from deep space containing a transmission code thirty times stronger than galactic background noise. Dr. Kip Troitsky tells Scully that only a handful of radio telescopes actively search for such signals. Scully searches through airline manifests and finds one containing Mulder's pseudonym, "George E. Hale." That flight was bound for Puerto Rico. Scully's progress is slowed when a hurricane strikes the island. She grows even more concerned when she realizes other FBI agents are following her.

Mulder and Jorge listen to the reel to reel tapes as the force of the hurricane intensifies. Suddenly, Jorge hears noises that terrify him. He runs from the building. Mulder runs after him, but after a short search discovers the man's dead body, his expression frozen in fear. Feeling more isolated than ever, Mulder records his thoughts into a tape recorder. He wonders aloud what he would do if he did indeed come face to face with extraterrestrial life. Moments later, an intense, blinding force rocks the building. Mulder watches, horrified, as what appears to be an alien being walks towards him. He is engulfed in a blinding light.

When Mulder regains consciousness, Scully is at his side. They soon realize that the Blue Beret team has arrived. Confident the Berets will kill them, the pair scramble for a nearby jeep and head into the wilderness. The Berets open fire, striking the jeep. Mulder outmaneuvers them and escapes down a roadway. When he returns to Washington, Mulder is reprimanded by Skinner for missing work. Mulder counters that his phone was tapped illegally. Mulder is allowed to keep his job. Later, he and Scully listen to the reel to reel tape, only to realize it is blank.