The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war’s aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section’s Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military’s 501st Secret Unit. Batou, a man with the “eye that does not sleep,” suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute’s murder. Motoko herself is being watched by the 501st Secret Unit’s head Kurutsu and cyborg agents.

Mima Kirigoe is a singer who leaves her trio to become an actress, a career move that angers her fans, who prefer to see her as the pop idol. Plagued by self-doubt and tormented by humiliating compromises, she begins to be stalked, in her waking and sleeping moments, by an alter ego who claims to be “the real Mima”, until she collapses into madness as her coworkers are brutally slain around her.

Childhood friends Tetsuo and Kaneda are pulled into the post-apocalyptic underworld of Neo-Tokyo and forced to fight for their very survival. Kaneda is a bike gang leader, and Tetsuo is a member of a tough motorcycle crew who becomes involved in a covert government project called Akira. But a bloody battle ensues when Kaneda sets out to save his friend.