Robert Patrick Modell, aka "Pusher," has recovered from his injuries and escaped from a prison hospital. Mulder and Scully lead the manhunt even as Modell may be using his powerful mind-control capabilities to target Fox for revenge.
Scully undergoes hypnosis to recall her experiences on the bridge where the group of abductees was burned alive. Krycek provides the consortium with a vaccine for the black oil and tells Mulder of the planned colonization and alien rebels.
In 1990 Mulder investigates the death of a man who disappeared in 1952 before he could be charged in a series of bizarre killings. The retired agent who worked the 1952 case recounts the facts to Mulder and the connection to his father.
Mulder goes undercover to infiltrate a militia group armed with a deadly pathogen and wanted for domestic terrorism. Scully becomes suspicious when Mulder lets a suspect escape but she learns that his assignment may be a suicide mission.
Mulder is taken hostage with the office coworkers of a man who claims the boss is a monster controlling their minds and turning them into zombies. Mulder and Scully believe the man to be delusional until they begin to see the same things.
During a chess tournament, a young boy becomes the center of an investigation concerning the alien mythology. Meanwhile a face from Agent Mulder's past causes friction in his relationship with Agent Scully.
An anonymous tip finally brings Mulder and Scully to the mecca of all UFO lore, Area 51. But when the agents witness the flight of a mysterious craft, their lives are profoundly and perhaps irrevocably altered.