In January 2029, a terrorist bombing of an aircraft occurs in the suburbs of Newport City. Section 9, led by Aramaki, receives a request from the U.S. military intelligence division to jointly investigate the incident. The prime suspect is known as the "Pyromania," a broker for a cyber virus called "Fire Starter," which implants false memories.

After an intense cyber battle, Kusanagi successfully apprehends Pyromaniac. However, the body of the terrorist suspected to be Pyromaniac is later discovered at the crash site of a plane explosion. While Pyromaniac's cyberbrain is being analyzed, Kusanagi and her team are removed from the joint investigation and reassigned to escort Colonel Hozumi.