One week later. Mulder and Scully, now are working in antiterroristic department of FBI and looking for a bomb in Federal building. But they accidentally find bomb in a building opposite the Federal building and help in evacuation. But bomb shortly
after detonates, killing Special Agent-in-Charge Darius Michaud, who was 'trying' to defuse it, and destroying the building.

The powers that be in FBI try to pin the blame on Mulder and Scully for the explosion and death of 4 persons, and endeavor to split the partners up. Scully tells Mulder, she is going to quit FBI. But in Washington Mulder is contacted by Dr. Kurtzweil, his father's old friend, who explains him that bomb blast in Dallas was part of cover up by members of the 'gouvermen't. The reason why bomb was in that building, and not in Federal one, is quarantine office, where were bodies, dead bodies. Adding
substance to Dr Kurtzweil claims, given credence when Scully's autopsy of one of the fireman can't produce a cause of death.

Mulder manages to convince Scully to help him investigate the case as he needs her. They undercover a sinister conspiracy by the shadowy syndicate to aid aliens in their colonization plans. They find huge corn fields in desert, giant Jiffy Pop poppers, bee
farm, all prepare for beginning of colonization.

But even the syndicate ate caught out, as the black oil has mutated into a virus that affects humans using them to create a new alien form. A virus for which there is no cure, save for a week antidote developed by the Russians.

Scully gets immediately transfer to Salt Lake City, but she decides really to quit FBI this time. Mulder tries to convince her not to quit, and to stay with him to help him in further investigation. Than he 'kisses' her, but in very same moment a bee strungs her. In the movie we for a first time see kiss between Scully and Mulder. It isn't real kiss, but after 5 season without any, it was ok. Mulder calls 911, but syndicate members indercept call and kidnap Scully and shoot Mulder. They take Scully to the secret installation in Antarctica.

With help of Lone Gunmen Mulder leaves hospital and attempts to find Dr Kurtzweil for more information, but instead meets the WMM, who gives him Scully's location and small amount of Russian antidote. Mulder tracks Scully to the installation in Antarctica, gaing entry via tunnel in the ice. He stumbles across thousands of cryo-tubes contain people infected with the virus, gestating the new alien life form. He locates Scully and injects the antidote, some of which gets into the system. Mulder and Scully flee the installation just in time as it turns out to be an alien craft. As they collapse at a safe distance, Mulder watched in awe as the craft flies over head and disappears into the clouds, moments later Scully regains consciousness.

Back in Washington, Scully and Mulder are on review again. They new more facts now, but all evidence they had are destroyed. Except one - bee which strunged Scully. Newspapers publics news about outbreak fatal hanta virus in Northern Texas. Scully changes her mind about leaving Mulder, so, they'll still work together with paranormal...

And last scene. Helicopter lands at the syndicate's new corn/bee farm in desert in North Africa. CSM steps out and walks toward Strughold. They discuss the new bee farm and the progress of their plans. CSM hands a telegram to the other man informing them that the X-files have been reopened.