E.B.E. is a taunt, tightly plotted story that is the true beginning of the vaunted X-Files Mythology Story Arc. It begins over the skies of Iraq, where an Iraqi fighter pilot shoots down a UFO. The United States military manages to get a hold of the wreckage. Several days later, Mulder and Scully are working a case in Tennessee where a truck driver had experienced what appeared to be a UFO encounter. While interviewing the trucker, they notice that he is sick, with a bad cough. The trucker, named Ranheim, says his condition started since his encounter with the UFO. But their interview comes to an abrupt end when the local sheriff releases Ranheim and all but kicks Mulder and Scully out of the station house. Figuring that somebody higher up had gotten to the sheriff, Mulder and Scully check in with the Lone Gunmen. E.B.E. is the very first appearance of this trio, and they certainly make an interesting first impression on Scully, whom Byers takes a twenty-dollar bill from and rips up, revealing a magnetic strip that he claims the government is using to keep track of people.

Although the Lone Gunmen can offer no new leads, Scully and Mulder do discover something disturbing: they are being spied on. Scully's pen, which she lent to a seemingly harmless woman at the airport, contains micro-sized electronic surveillance equipment. When Mulder contacts Deep Throat (Jerry Harding) to get some answers, Deep Throat gives him a file about the Iraqi UFO encounter. Meanwhile, Scully has found out that the truck driver, Ranheim, was not who he said he was. He was actually a former Special Forces soldier who served in Northern Iraq during the Gulf War. Putting the pieces together, Mulder realizes that Ranheim was transporting either pieces of the wreckage or the pilot of the Iraqi UFO on board his truck, and that may be why he was the focus of the UFO encounter the other night. Just before they set out to locate the truck, which is heading cross country once more, Mulder gets a surprise visit from Deep Throat, who offers rock-solid proof in the form of a photograph of a UFO hovering over a military base.

But Scully is not so sure if Deep Throat can be trusted; for all she knows, he might be the one behind the bugging of the X-Files agents' office and homes, and he may well be leading Mulder on a wild goose chase. This opinion causes some friction between Mulder and Scully, until he has the photo checked out by a lab--and it turns out to be a phony. Now completely on their own, the agents doggedly chase Ranheim and his truck across the country, hoping that the answers to this puzzling and disturbing case can be found in his mysterious cargo.

The reknown paranoia of The X-Files swings into full gear with E.B.E., which stands for Extraterrestrial Biological Entity. Can Deep Throat truly be trusted? Or is he merely another enemy seeking to obstruct and ultimately destroy the X-Files? Glen Morgan and James Wong wrote the compelling script, which keeps you on the edge of your seat right up to the very end.