S1E7 · Ghost in the Machine

In the Crystal City, Virginia, headquarters of the software company Eurisko, founder Brad Wilczek and chief executive officer Benjamin Drake argue about downsizing measures. After Wilczek leaves, Drake writes a memo proposing to shut down the Central Operating System (COS), a computer which runs the Eurisko Building. Seeing this through a surveillance camera, the COS sets up a trap and lures Drake into a bathroom, locking the door behind him. Drake tries to use his keycard to open it, but it rejects the card. When he inserts a manual override key, he is fatally electrocuted.

FBI Agent Jerry Lamana, Fox Mulder 's former partner in the Behavioral Analysis Unit, approaches him and Dana Scully for help in investigating Drake's murder. 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 COS records her contact information before reactivating the elevator. While examining the crime scene, the agents meet Claude Peterson, the Eurisko Building's systems engineer. Later, Lamana steals Mulder's profile of the supposed killer and presents it under his name; an outraged Mulder confronts him afterwards.

Mulder and Scully question Wilczek, who denies any involvement in the murder. Scully initially doubts Wilczek's involvement but finds that his voice matches a speaking clock Drake received before his death; Lamana sets out to arrest him. Meanwhile, Wilczek fails to access the COS from his home computer. Concerned, he travels to the Eurisko Building, followed by Lamana. There, he is still unable to access the COS, but discovers that it has learned to talk. Lamana arrives but is killed when the COS causes his elevator to crash.

Mulder meets with Deep Throat, who explains that the COS is an artificial intelligence developed by Wilczek, and that the Department of Defense is trying to acquire it. Mulder also meets with Wilczek, who has falsely confessed to Lamana's murder. Mulder convinces Wilczek to develop a computer virus that can destroy the COS. Scully doesn't accept Mulder's belief that the COS is sentient, but later discovers the machine hacking into her computer. She joins Mulder at the Eurisko Building to help him destroy the machine.

The COS hinders the agents as they make their way inside. When it shuts down the building's power, Scully climbs through the air vents and is almost pulled into a giant fan, but manages to destroy it. Meanwhile, Mulder is permitted into the COS' control room by Peterson. However, Peterson reveals himself as a mole for the Defense Department and tries to stop Mulder uploading the virus. Scully arrives and holds Peterson at gunpoint, allowing Mulder to upload the virus and destroy the COS.

Mulder again meets with Deep Throat, who explains that Wilczek is being detained by the government at an undisclosed location. When Mulder asks if the COS survived, Deep Throat assures him the virus left no trace of the program and that scientists from the Defense Department examined the machine to no success. At the Eurisko Building, Peterson directs a team attempting to recover the COS, but is told by his superiors to destroy the machine in six hours. Unbeknownst to Peterson, the COS comes back to life and watches as he says to himself, "I'm going to figure this thing out even if it kills me".