In the episode's prologue,
Fox Mulder narrates a history of
NASA's
Voyager program and the now-defunct
High Resolution Microwave Survey, which sought to contact
extraterrestrial life in outer space. At the Survey's abandoned
observatory in
Arecibo,
Puerto Rico, the equipment inside suddenly activates, indicating a response from an alien intelligence. Since the
closure of the X-Files, the
FBI has reassigned Mulder to a low-level
wiretap while his former partner,
Dana Scully, has returned to teaching at the
FBI Academy. The two have a discreet meeting at the parking lot of the
Watergate Hotel, where Mulder admits that he has been doubting his belief in the paranormal since
Deep Throat's assassination. Mulder flashes back to the night when his sister,
Samantha, was abducted. Mulder is summoned to a meeting with
Richard Matheson, a
U.S. senator who is a patron for his work. Matheson directs Mulder to Arecibo, assuring the agent that he will try to hold off a
Blue Beret UFO retrieval team said to be headed there in twenty-four hours. Arriving at the Survey station, Mulder discovers a frightened Puerto Rican man, Jorge, who cannot speak English but draws a picture of an alien he claims to have seen. Meanwhile, Scully, unaware of Mulder's whereabouts, goes to his apartment looking for him. Reviewing a list of flights from
Washington, Scully recognizes one of Mulder's personal heroes' names and tracks him down to Puerto Rico. Mulder discovers a signal, possibly originating from an
extraterrestrial intelligence. During a storm, Jorge panics and runs outside; Mulder finds him dead of fright. When Scully goes to an airport to fly to Puerto Rico, she realizes she's being tracked by a couple but manages to lose them. Meanwhile, as Mulder examines Jorge's corpse, the room shakes. The door opens and the shadowy figure of an alien appears; Mulder tries to shoot it, but his gun malfunctions and he passes out. Scully wakes Mulder up the next morning, finding him excited about the readouts and tapes of the signals—the proof of aliens he has sought for so long. However, the Blue Beret team arrives, forcing them to flee with only a tape reel. Upon his return to Washington, Mulder is admonished by Assistant Director
Walter Skinner and the
Smoking Man for his actions. Mulder claims he still has enough evidence with the days missed to prosecute the subject of his assigned wiretap, and that his own phone calls were being monitored. Skinner then demands that the Smoking Man leave the room, and decides to not discipline Mulder. Investigating the tape reel, Mulder finds it
blank due to a power surge during the storm, but vows to continue his work regardless. == Production ==