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Directed by William Graham
Near the border between Iraq and Turkey, an Iraqi fighter pilot shoots down a UFO. Later, a truck driver in Tennessee named Ranheim sees another UFO, and starts shooting in the dark. Mulder and Scully investigate the sighting, but are turned away, causing them to turn to the Lone Gunmen, a trio of conspiracy theorists that Mulder is friends with. Meanwhile, Deep Throat informs Mulder of the Iraqi UFO incident.
Investigation of Ranheim's truck reveals discrepancies in his cargo, causing Mulder and Scully to attempt to track it down. After putting up with some attempted manipulation from Deep Throat and attempts to spy on them, they track down Ranheim and his truck in Washington state, finding out that he was transporting the UFO's pilot (an "extraterrestrial biological entity", or an E.B.E.) to the town of Mattawa, Washington.
Here, Mulder and Scully infiltrate the power plant where they believe the E.B.E. is being held. There, they learn from Deep Throat that, after the Roswell crash, the world's great powers made a secret agreement to destroy any live extraterrestrials. Deep Throat himself is one of three people who personally killed an alien, and his guilt over doing so is part of the reason why he is helping Mulder and Scully. He then lets them go free.
- Artistic License History: An arguable case. Three of the powers named by Deep Throat in the post-Roswell agreement on ET policy are the People's Republic of China and the two Germanies. The Chinese Civil War was still ongoing in 1947 (the year of the Roswell crash), with the PRC only recognized by the Soviet Union and the Kuomintang still holding the lion's share of China's territory and population, while East and West Germany were still the occupied territories of, respectively, the Soviet Union and the Western Allies. However, it's not stated the exact year the agreement was made; if it were made in 1949 or after, then all three of those countries would have been around to sign it.
- Being Watched: Mulder and Scully. Scully's pen gets bugged, and Mulder's apartment is under surveillance as well.
- Bat Signal: Blue glowing light coming out of Mulder's apartment to make contact with Deep Throat.
- Conspiracy Theorist: The Lone Gunmen (Byers, Frohike, and Langly) were introduced in this episode. And of course, there's Mulder.
- Even Nerds Have Standards: Even the Lone Gunmen are skeptical of Mulder's ideas, but they do enjoy them.Byers: That's what we like about you, Mulder. Your ideas are weirder than ours.
- Government Conspiracy: This was the first episode written specifically for the series' Myth Arc.
- Insufficiently Advanced Alien
- Inspired by : Writer Glen Morgan cited All the President's Men as a major inspiration for the episode.
- Make the Bear Angry Again: The Lone Gunmen speculate that the radical Russian nationalist Vladimir Zhirinovsky is a CIA plant meant to do this.
- Mysterious Informant: Deep Throat.
- Myth Arc
- Properly Paranoid: Scully was right that Mulder shouldn't blindly trust Deep Throat.
- Tempting Fate: Scully gives a scathing commentary on the delusional paranoia displayed by Mulder's conspiracy theorist pals, specifically their belief that the government is currently (and capable of) tracking their movements. Midway through this rant, she realises it's happening to her.
- The Only One I Trust: The first of many times Scully and Mulder will say it.Scully: Mulder, you're the only one I trust.
Mulder: Then you're gonna have to trust me.
- Averted with Mulder and the Lone Gunmen, as Langly turns on a tape recorder when Mulder calls and falsely claims to have turned it off. (Mulder calls Langly on it, though.) The FBI has had no shortage of Agent Provocateur operations, after all.
- Villain Respect: Deep Throat says he had their best people work on the fake photo, so he is most impressed that Mulder was able to figure out the truth.
- We Will Not Use Photoshop in the Future: Mulder is married to the idea that Deep Throat's UFO photo is real.
- What the Hell, Hero?: Mulder is positively outraged that Deep Throat tried to deceive him. Deep Throat hits back that he puts his life on the line every time he makes contact with Mulder.
- Who Shot JFK?: Langly claims to have had lunch with the real assassin, who purportedly claimed to be dressed as a cop on the grassy knoll.
Mulder: I'm wondering which lie to believe.