The film opens in 35,000 B.C., in what will become North Texas. Two cavemen hunters encounter a large extraterrestrial life form in a cave, which kills one and infects the other with a black oil-like substance. In 1998, in the same area, a boy falls into a hole and is also infected by a black substance which seeps from the ground. Firefighters who enter the hole to rescue him do not come out. A team of men wearing hazmat suits arrive and extract the bodies of the boy and the firefighters. Meanwhile, FBI Special Agents Fox Mulder and Dana Scully, while 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. However, he simply waits for the bomb to detonate.
Mulder and Scully are later chastised because, in addition to Michaud, four other people were in the building during the bombing. That evening Mulder is accosted by a 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 is able to examine one of the victims, finding evidence of an alien virus. Meanwhile, the Cigarette Smoking Man goes to Texas, where Dr. Ben Bronschweig shows him one of the lost firefighters, who has an alien organism residing inside his body. He orders Bronschweig to administer a vaccine to it, but to burn the body if it fails. Later, the alien organism unexpectedly gestates and kills Bronschweig. Mulder and Scully travel to the crime scene in Texas, encountering the boys whose friend fell into the hole. Following their direction, they find the site has been hastily turned into a new playground. The pair follow some white gasoline tankers to a large cornfield surrounding two glowing domes. Inside the domes, grates in the floor open and swarms of bees fly out. The agents flee, chased by black helicopters, but manage to escape.
After returning to Washington, D.C., Scully attends a performance hearing, after which she is transferred. Mulder is devastated to lose his partner. The two are about to share a kiss when Scully is stung by a bee which had lodged itself under her shirt collar, she quickly falls unconsciousness while Mulder calls paramedics but the driver of the ambulance shoots Mulder and whisks Scully away. Mulder, not severely injured, slips out of 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, along with a vaccine against the virus that has infected her. As Mulder leaves, the Well-Manicured Man kills himself in a car bomb, before his betrayal of The Syndicate is discovered.
