In the Virginia headquarters of the software company Eurisko, founder Brad Wilczek and C.E.O. Benjamin Drake argue about the latter's downsizing measures. After Wilczek leaves, Drake writes a memo proposing to shut down the Central Operating System, a computer that runs the building. Seeing this through a surveillance camera, the C.O.S. sets up a booby trap, luring Drake into a bathroom with an overflowing faucet and locking the door behind him. When Drake tries to use an electronic key to open it, a massive electric current sends him flying across the room, killing him.
Jerry Lamana, a former partner of Mulder's, approaches him and Scully for help in investigating the murder. Lamana hopes to use the case to recover his troubled career, due to Drake's connections with the Attorney General; Mulder later explains to Scully that Lamana's need for recognition stems from a case he bungled in which a federal judge was injured. On their way up to Drake's office, the agents' elevator stalls, causing Scully to call the front desk for help. As she identifies herself, the C.O.S. downloads her contact information. At the crime scene, the agents meet Claude Peterson, head of building security, who discovered the body.
Lamana steals Mulder's profile of the supposed killer, presenting it under his name; an outraged Mulder confronts him afterwards. The agents later question Wilczek at his home. Scully initially doubts Wilczek's involvement in the murder, but finds that his voice matches a 4-1-1 call Drake received before his death; Lamana sets out to arrest him. Meanwhile, Wilczek fails to access the C.O.S. from his home computer. Concerned, he travels to Eurisko's headquarters, followed by Lamana. There, he is still unable to access the C.O.S., but discovers it has learned to talk without a voice synthesizer. Lamana arrives, but is killed when the C.O.S. causes his elevator to crash.
Mulder meets with Deep Throat, who says that Wilczek developed an artificial intelligence that the Defense Department is trying to acquire. Mulder also meets with an imprisoned Wilczek, who has falsely confessed to Lamana's murder. Mulder convinces Wilczek to develop a computer virus that can destroy the intelligence. Scully doesn't accept Mulder's belief that the C.O.S. is sentient, but later discovers the machine hacking into her computer. She joins Mulder at the Eurisko Building, agreeing to help him destroy the machine. The C.O.S. tries to obstruct and harm the agents as they make their way inside.
When the C.O.S. shuts down the building's power, Scully climbs through the air vents; the C.O.S. nearly blows Scully into a giant fan, which she eventually destroys. Meanwhile, Mulder is permitted into the C.O.S.' control room by Peterson. However, Peterson reveals himself as a mole for the Defense Department and tries to stop Mulder from uploading the virus. Scully arrives and holds Peterson at gunpoint, allowing Mulder to destroy the C.O.S. with the virus.
During a second meeting with Deep Throat, Mulder recounts that Wilczek is being detained by the government at an undisclosed location. When Mulder asks if the C.O.S. could have survived, Deep Throat assures him the virus left no trace of the C.O.S' artificial intelligence. He also tells Mulder that scientists from the Defense Department have been unsuccessfully examining the machine for any remaining signs of the program. Deep Throat believes the machine to be "dead". At the Eurisko Building, Peterson, directing a team attempting to recover the C.O.S., is directed by his superiors to destroy the machine in six hours. Unbeknownst to Peterson, the C.O.S. comes back to life and watches him as he says, "I'm going to figure this thing out if it kills me."
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