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The X Files

In 35,000 B.C. during the Ice Age, in what will become North Texas, two cavemen hunters encounter an extraterrestrial life form in a cave, which kills one and infects the other with a black oil -like substance. In 1998, a boy falls into a hole and is infected by the black oil that seeps from the ground. Firefighters who enter the hole to rescue him do not come out. A team of men wearing hazmat suits later extracts the bodies of the boy and the firefighters. Meanwhile, FBI Special Agents Fox Mulder and Dana Scully, investigating a bomb threat against a federal building in Dallas, discover the bomb in a building across the street. As the building is evacuated, Special Agent in Charge Darius Michaud remains, ostensibly to disarm the bomb. Instead, he simply waits for the bomb to detonate.

At the Office of Professional Review hearing supervised by FBI Assistant Director Jana Cassidy, Mulder and Scully are chastised because the firefighters and the boy were also in the building during the bombing. That evening, Mulder is accosted by paranoid doctor Alvin Kurtzweil, who explains that the "victims" were already dead and that the bombing was staged to cover up how they died. At the hospital morgue, Scully examines one of the victims, finding evidence of an alien virus. Meanwhile, The Smoking Man goes to Texas, where Dr. Ben Bronschweig shows him one of the lost firefighters, who now has an alien organism residing inside his body. The Smoking Man orders Bronschweig to administer a vaccine to it, but to burn the body if it fails. Later, the alien organism gestates and kills Bronschweig.

Mulder and Scully travel to the site of the hole in Texas, where they find it has been hastily turned into a new playground, and encounter the boys whose friend fell in. Driving in the direction the boys indicated, the pair encounters a train of white gasoline tankers and follows it to a cornfield surrounding two glowing domes. Inside the domes, grates in the floor open and swarms of bees fly out, overwhelming the agents. They flee through an adjacent cornfield, chased by black helicopters, and escape when the helicopters disappear.

In D.C., Scully attends another OPR hearing; meanwhile, Mulder meets with Kurtzweil to obtain more information. Scully arrives at Mulder's apartment to tell him she has been transferred to SLC but plans to resign from the FBI. The two are about to kiss when Scully is stung by a bee that had lodged itself under her shirt collar. She falls unconscious while Mulder calls paramedics, but the ambulance driver shoots Mulder and takes Scully away. She is seen later in an isolation unit being loaded onto a plane. An unconscious Mulder is picked up by another ambulance. Not severely injured, he slips out of the hospital with the help of The Lone Gunmen and FBI Assistant Director Walter Skinner. He then meets a former adversary, the Well-Manicured Man, who gives him Scully's location and a vaccine against the virus that has infected her. As Mulder leaves, the Well-Manicured Man shoots his driver and then kills himself in a car bomb before his betrayal of The Syndicate is discovered.

48 hours later, Mulder finds Scully in an underground facility in Antarctica, which also contains many humans suspended in ice-like enclosures. He breaks Scully's confinement and uses the vaccine to revive her, but this disrupts the facility, and the cocooned aliens begin trying to escape. After Mulder and Scully escape to the surface, an alien vessel emerges from beneath the ice and travels into the sky. Mulder watches it disappear into the distance as Scully regains full consciousness.

At another hearing, Scully's testimony is disregarded, and evidence in Texas is destroyed. To the hearing moderator, she hands over the only remaining proof of their ordeal—the bee that stung her—while noting that the FBI is currently unable to investigate this evidence. Outside, Mulder reads an article about the domes and crop fields in Texas that have been covered up. Scully reveals that she is willing to continue working with him: "If I quit now, they win." At another crop outpost in Tunisia, the Smoking Man warns Conrad Strughold that Mulder remains a threat, explaining what Mulder has found out about the virus. He then hands him a telegram revealing that the X-files unit has been reopened.