S1E2 · Deep Throat

In southwestern Idaho, near Ellens Air Force Base, military police raid the home of Colonel Robert Budahas, who has barricaded himself inside after stealing a military vehicle. The authorities find Budahas trembling and covered in rashes.

Four months later, FBI agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) meet at a Washington bar to discuss the case. Mulder explains that Budahas, a test pilot, has not been seen since the raid and the military will not comment on his condition; the FBI has refused to investigate. Mulder claims that six other pilots are missing at the base, which is subject to rumors about experimental aircraft. While using the bar's restroom, Mulder is approached by a mysterious informant named " Deep Throat " (Jerry Hardin), who cautions him to avoid the case. He claims that Mulder is under surveillance, which later proves to be true.

Mulder and Scully travel to Idaho and meet with Budahas' wife, Anita, who claims her husband exhibited erratic behavior before his disappearance. She tells them about a neighbor–whom the agents visit–whose husband is also a test pilot who has been behaving oddly. Scully makes an appointment with the base's director, Colonel Kissell, but he refuses to talk when they visit his home. They are subsequently approached by Paul Mossinger, who identifies himself as a local reporter and refers them to a local UFO -themed diner; there, they discuss UFOs with the owner, who believes she has witnessed several nearby.

Visiting the base that night, the agents witness a mysterious aircraft performing seemingly impossible maneuvers in the sky. They flee when a black helicopter approaches, seemingly in pursuit of Emil and Zoe, a trespassing teenage couple. As Mulder treats Emil and Zoe to a meal at the diner, they tell the agents about the lights and how they believe the UFOs are launched from another nearby base. Meanwhile, Budahas is returned to his home with no memory of what happened. After leaving the diner, Mulder and Scully are confronted by black-suited agents, who destroy the photographs they have taken and order them to leave town.

An indignant Mulder sneaks onto the base with help from Emil and Zoe. He sees a triangular craft fly overhead and then is captured by soldiers who tamper with his memory. Meanwhile, Scully re-encounters Mossinger, whom she discovers is actually a security operative for the base. At gunpoint, she forces him to guide her to the base and exchanges him for Mulder. Having been denied the truth about the base, Mulder and Scully return to Washington. Days later, Mulder encounters Deep Throat while jogging at a local track. Mulder asks if "they" really are present on Earth; Deep Throat responds that "they have been here for a long, long time."