Mulder and Scully are approached by Special Agent Jerry Lamana, who is on probation for mishandling an important case. Lamana explains that he has been assigned to investigate the murder of Benjamin Drake, the CEO of a Fortune 500 company called Eurisko. Drake was electrocuted when he fell victim to an elaborate boobytrap devised by someone with intimate knowledge of the Central Operating System (COS) at Eurisko's high rise headquarters. Afraid of mishandling yet another important case, Lamana successfully lobbies Mulder and Scully's expertise.
     The agents are told by Peterson, the Eurisko building's system engineer, that one of the few people who has access to the building's sophisticated control center is Brad Wilczek, the 30-year-old founder of the company and Drake's arch enemy. Using a voice analyzer, Scully determines that Wilczek disguised his own voice electronically and telephoned Drake moments before his death... playing a key role in the boobytrap.
     Lamana drives to the Eurisko building to make the arrest. The elevator Lamana rides in reaches the 29th floor and suddenly drops at fantastic speed, crashing into the ground.
     Mulder learns from Deep Throat that Wilczek had been hard at work on Artificial Intelligence-the development of a thinking machine. Though Wilczek is arrested for the deaths of Drake and Lamana, and even signs a confession, Mulder believes him innocent.
     From his jail cell, Wilczek admits to Mulder that COS is an intelligent machine. He explains that when Drake made overtures to shut the system down, COS eliminated him in self-defense.
     Mulder convinces Wilczek to develop a computer virus that will shut down the system. Armed with the virus, Mulder and Scully gain entrance to the Eurisko building. COS anticipates their every move and turns the building's electrical systems against them.
     With Peterson's assistance, Mulder makes his way to the main control room. As Mulder is about to insert the computer disk into the system, Peterson pulls out a gun and demands he stand back. Peterson admits he is an operative for the Defense Department-a government agency eager for Artificial Intelligence technology. Scully enters and pulls her gun, gaining the upper hand. Peterson drops his weapon.
     Mulder inserts the computer disk and engages the virus. COS shuts down forever... or does it?