Several heavily-armed crack dealers receive an anonymous telephone call alerting them to the whereabouts of a hated enemy. The men all converge on a diner, but none find their target. Two deputy marshals receive a similar anonymous tip, alerting them about a Colombian fugitive in the same diner. The marshals enter the diner and order everyone onto the floor. Drug dealers draw their weapons and a fierce gun battle ensues.

As the agents observe the aftermath of the shoot-out, Mulder pulls a tarp off the face of Donald Gelman, one of the co-inventors of the Internet. Gelman had been working at his laptop inside the diner when the shooting broke out and became trapped in the cross-fire. Mulder sneaks Gelman's laptop under his jacket and brings it back to Scully's car. He finds a blank CD in the laptop drive, which when placed inside Scully's CD-player emits music from The Platters' Twilight Time. Puzzled, Mulder brings the CD to the Lone Gunmen for further analysis. When they are unable to crack the disc's security code, Scully suggests they check Gelman's e-mail log. They find a message containing a standard ID number for a shipping container. The message is signed by someone named Invisigoth.

The agents track the number to a container yard. A figure springs from the darkness, zaps Mulder with a stun-gun, and runs off into the night. Scully apprehends the suspect, Esther Nairn, a gorgeous young woman with a nose ring, and escorts her back to the container, which is brimming with sophisticated computer equipment. Esther's attention is diverted to one of the monitors. She tells the agents that an armed Department of Defense satellite has locked onto their location. Despite the farfetchedness of the tale, Mulder convinces Scully they must leave the area immediately. Shortly thereafter, a strange green light descends from the heavens and destroys the shipping container.

Mulder concludes that Donald Gelman realized his lifelong dream: the construction of a sentient artificial intelligence, a computer program with its own consciousness. Esther confirms Mulder's suspicion, describing how Gelman unleashed the program onto the Internet so it could evolve--much like the primordial slime from which mankind evolved. She tells the agents that the AI monitors all communication, and will destroy her the moment it locks onto her location. Esther also reveals that Gelman was in the process of creating a special virus program, nicknamed "Kill Switch," that would hunt down and destroy the rogue system. Instead of simply destroying Gelman with a laser from above, Esther is convinced it killed its creator with a dozen crack dealers in an effort to show off its sense of humor. She also believes the virus is holed up on a computer somewhere--and the only way to kill it is to find and destroy its safe house.

By accessing government files, Mulder locates a suspicious T3 line, one that would be needed by the AI to access the Internet. He traces the cable to an abandoned farm on which sits a trailer. Meanwhile, Esther gets the jump on Scully and forces her at gun point to drive to an isolated location where she hopes to find one of her colleagues, a man named David Markham. Esther exits the car and begins crying at the site of a demolished house. During her absence, Scully manages to unshackle her handcuffs. Esther gives Scully back her gun and asks her to "put her out of her misery." Esther then admits to Scully that she and David had planned to download their consciousness and enter the AI. But Gelman forbade the idea.

Mulder gains access to the trailer housing the T3 line. Inside he discovers David Markham's body, his face concealed by a virtual reality mask. Suddenly, several crab-like droids spring from the jungle of cables and constrain Mulder. Mulder experiences strange visions involving nurses in a 1940s hospital who threaten to amputate him, limb by limb, unless he reveals the location of Kill Switch. Meanwhile, the AI pinpoints Scully and Esther in their car near a turntable drawbridge. The pair become trapped and, at Scully's urging, Esther tosses the laptop into the water. Moments later, a green laser blasts the water.

Scully and Esther climb into the trailer where Mulder is bound by the crab-droids. Several of the robotic creatures attack, and Scully dispatches them with her revolver. Scully finds Mulder, his head encased in the virtual reality mask (the source of his strange visions). Esther produces the CD, and Scully gives the AI what it wants, inserting the disk into a drive. The AI releases Mulder, and Scully drags him outside. Esther accesses a keyboard and instructs the satellite to lock onto the trailer's coordinates. When Scully reenters the trailer, she finds Esther wearing the virtual reality helmet, the body of her beloved David nearby. Scully races from the trailer, and Esther instructs the AI to upload. Moments later, the green laser destroys the trailer. When Mulder recovers, he tells Scully that Esther's consciousness may have joined the AI.