Mulder and Scully come to investigate when an Iraqi pilot supposedly shoots down a UFO and encounter a government cover-up which will do anything to divert the agents from the truth.

While Mulder looks for typical UFO signs on the crash site, Scully looks for tangible evidence. He finds that while they were looking for the evidence, they lost quite a substantial amount of time. Later they find out about a truck driver who lost power on a road and saw a UFO. When they try to question him a very uncooperative government agent enters and prevents any further questioning. Mulder though seems convinced that this truck was transporting an Extraterrestrial Biological Entity.

Scully has every reason to believe that Mulder is nuts when he introduces her to a government watchdog group named 'The Lone Gunmen' who also publish a magazine on unexplained phenomena. Scully is completely skeptical and believes they are just paranoid (Byers is convinced that a $20 bill contains a magnetic strip which the government uses to track you and Langly tapes every phone call he makes) but she later finds some surveillance equipment in her pen which kind of makes her believe them.

When Mulder contacts Deep Throat for help, he tells Mulder he is on a very dangerous path and hands him an envelope containing a picture of a UFO. Mulder believes this is the best photographic evidence he has ever seen. Scully is not convinced at all claiming the photo is bogus. Mulder thinks Scully just can't open her mind but when the photo is analysed it is proved to be a fake.

Mulder contacts Deep Throat again who admits that the photo was fake and was ' prepared by our very best' while stating that there are some secrets that remain secret. It seems that now, Scully is the only one Mulder can trust completely.

Scully is able to find out the whereabouts of the truck Mulder believes is transporting an E.B.E so they track it down followed by two officials who they manage to avoid and are suddenly stopped by a bright flash. When the flash stops they find the truck straight ahead and empty and contains what looks like a small cubicle which Mulder thinks they transported the alien in. Again he is convinced that they were witness to a 'rescue mission' but again he is let down when there are no signs that this is a true close encounter.

Nevertheless they are manage to track down the truck driver who they see entering a high security building. With help from the Lone Gunmen, they are able to also gain access but when they are stopped by security Mulder runs off trying to locate the alien. Deep Throat appears who tells Mulder about a secret pact between nations that any surviving E.B.E should be killed. Deep Throat admits that he was one of the three men to have carried out the act.

While Deep Throat disappears into the fog, Mulder is left wondering which lie to believe...