A UFO crashes in Iraq. The craft and its occupants are brought to the USA, and then transported by undercover trucks to a governmental facility, followed by Mulder & Scully and another UFO. There, the surviving occupant is killed by Deep Throat following a secret international agreement.
E.B.E. : Extraterrestrial Biological Entity
In the first truely paranoid episode penned by masters Morgan & Wong (and thus highly quotable), Scully is shocked to discover the government isn't as benign as she believed it to be: the agents discover surveillance devices in Scully's pencil and in Mulder's apartment. We meet the legendary Lone Gunmen ("an extreme government watchdog group"), and already Frohike has a fall for Scully.
We never get to see the alien occupant the UFO -- after all, the entire episode can be explained without including aliens, the EBE story being only yet another layer of lies. But apparently the EBE was badly wounded after the crash and it was unable to use its ability to emit radiation (1X09: Fallen Angel, 3X15: Piper Maru). The UFO was flying over the border of Iraq and Turkey; UFO reports are common at war times or at sensible geographical zones, one more reason to think that the UFO could very well be an experimental military plane (Scully: "the only UFOs people are likely to see are secret military aircraft.'). After the crash, the USA recovered the craft and its occupant through a NATO base in Turkey (the USA are the main force behind the North Atlantic Treaty Organization and Turkey is a member that is thought of highly by the USA because of its strategic location). The craft is surrendered to military research (1X01: Deep Throat) and the EBE is executed.
The truck driver, Ranheim (real name Frank Druce) was working undercover for the military. He had already been in a Special Ops unit in Iraq during the Gulf War, which ended in 1991; he's been under treatment for some illness he contracted during that time, hence the persistant cough. It's likely this came from coming into contact with UFOs, which can emit radioactivity (4X17: Tempus Fugit); or he was victim of a biological weapon that was used or tested there, perhaps even Black Cancer itself (4X10: Terma). Mulder makes the connection with Gulf War Syndrome, the real illness whose very existence has been debated, and suggests it might have been caused by UFOs. The Lone Gunmen talk about other theories on what caused it: "Agent Orange of the 90’s" (a synthetic herbicide harmful to humans used extensively in the Vietnam War, a form of chemical warfare), "Artillery shells coated with depleted uranium" (US troops used ammunition during the Gulf War).
The execution of the EBE
Deep Throat tells Mulder: "After the Roswell incident in 1947, even at the brink of the Cold War, there was an ultrasecret conference attended by the United States, the Soviet Union, the People's Republic of China, Britain, both Germanies, France and it was agreed that should any Extraterrestrial Biological Entity survive a crash, the country that held that being would be responsible for its extermination." This is in accord with 4X07: Musings of a Cigarette-Smoking Man; before executing an EBE, Deep Throat tells CSM: "Security resolution council 10-13 states 'Any country capturing such an entity is responsible for its immediate extermination'." This UN decision is in direct contradiction with the agreement with the Syndicate: two different organizations with different policies. The countries that voted the resolution are the five permanent members of the UN Security Council (USA, UK, France, Russia/USSR, China) plus Germany (at the time divided in western & eastern).
This Deep Throat character
Retrospectively, this episode, along with 1X23: The Erlenmeyer Flask, shows that in fact Deep Throat isn't an elder of the Syndicate. Deep Throat follows the orders of a UN resolution, secret may it be, and exterminates a living EBE, when he could have delivered it to the Syndicate. As CSM says in Musings, "A living EBE could advance Bill Mulder's project by decades." (this project is the discovery of a vaccine against the Black Oil). The Syndicate works above all governmental organizations, but Deep Throat seems to be affiliated to the US government.
Deep Throat was already watched by the Syndicate: his meetings with Mulder are photographed. He's under suspicion, but in this case he did what he was told or had to do: lie to Mulder. It wasn't in his purpose to lie to Mulder, he acknowledges M&S "are excellent investigators", to justify his doings. This foreshadows Deep Throat's murder in 1X23: The Erlenmeyer Flask.
The misinformation policy
Deep Throat provided Mulder with false data: when he had to, he could lie to him. The picture Deep Throat gave Mulder could only be proven fake under close examination: some serious work went into the making of this picture. We can thus suppose that Deep Throat was part of the Department of Defense's project of misinformation that is exposed in the Redux arc: spreading false information for the believers to look at the wrong place. This also establishes him as a mere executive of the Syndicate at best. Mulder starts suspecting he's unconsciously become part of this project: "Maybe they're using me against myself like you said before. That I want to believe so badly that I'd just accept the obvious conclusions and walk away."
The folder that Deep Throat gave Mulder contained a transcript of an intercepted iraqi communication, labelled "To: Commanding Officer, Majestic Project": this is a reference to the governmental Majestic Project, ex-MJ-12, that we'll hear from again in 2X25: Anasazi.
Scully: "From the trucker’s description, the shape he fired on could conceivably have been a mountain lion."
Scully: "The National Weather Service last night reported atmospheric conditions in this area that were possibly conducive to lightning."
Scully: "It is feasible that the truck was struck by lightning, creating the electrical failure."
Mulder: "It’s feasible."
Frohike [about Scully]: "She’s hot."
Byers [on CIA giving power to Russian social-democrats]: "You don’t believe that the C.I.A., threatened by a loss of power and funding because of the collapse of the cold war, wouldn’t dream of having the old enemy back?"
Byers: "We’re talking about a dark network, a government within a government, controlling our every move."
Byers: "That’s why we like you, Mulder, your ideas are weirder than ours."
"Those were the most paranoid people I have
ever met. I don’t know how you could think that what they say is even
"In our line, nothing is just what it
work for the Federal Bureau of
Investigation and we’re being bugged. What does that tell you?"
"A lie, Mr. Mulder, is most convincingly
hidden between two truths."
Deep Throat: "You're
quiet, Mr. Mulder."