The year is 2030. The world is rebuilding from World War III. In Neo-Tokyo, plans are being made to hold the next Olympics in the "old city"--where, thirty-eight years before, the first of the bombs fell. In the old city, a band of teenaged delinquents led by Kaneda encounter Number 26--a terrified child possessing extraordinary telekinetic abilities. As a result of the encounter, Kaneda and his friend Tetsuo become entangled in a power struggle between a mysterious organization led by a man known only as the Colonel and an underground resistance group, bent on stopping to the Colonel's activities.
Among the resistance, Kaneda meets Kay, her brother, Ryu and Ryu's closest subordinate, who finds and nearly kills a spy from the Colonel's organization. They are commanded by Nezu--a government official--and a powerful religious leader with precognitive gifts--Lady Miyako.
There is a number of children under the Colonel's control, each one possessing a unique talent and identified by a number marked on their hand. Another of the children is Akira, so powerful that since the war he has been suspended in cryogenic sleep.
The Colonel's chief medical advisor, called Doctor, subjects Tetsuo to painful electronic and chemical experiments. This awakens tremendous telepathic potential in the boy, who is dubbed Number 41. Unfortunately, a monstrous side of Tetsuo's nature also appears. With the ability to shrug off the most serious injuries, Tetsuo goes on a killing spree.
Eventually, he murders one of Kaneda's closest friends, then attacks Kaneda. This allows the Colonel to capture Kaneda and Kay.
Tetsuo finds it intolerable that Akira may be more powerful, and forces the Doctor to tell him where Akira is. Tetsuo is determined to seek Akira out and attacks the Colonel when he tries to stop him. The psychic children, who, like Lady Miyako fear Akira's power. They are worried about the disaster Tetsuo may unleash, and use their talents to help Kaneda and Kay escape. "Aided" by the same spy Ryu's lieutenant previously left for dead, pursue Tetsuo to the Olympic site, where Ryu and his lieutenant are working undercover.
The Colonel tries to prevent a disaster by unleashing his troops and scientists. A fight ensues. Tetsuo is attacked, but not harmed. Meanwhile, Akira's chamber temperature rises, apparently responding to Tetsuo's psychic energy.
Kaneda, Kay and the spy steal one of the army's flying platforms, but are unable to control it. The result is while trying to reach Akira'a chamber, the unlikely trio fly by an elevator platform carrying Tetsuo, Ryu and his lieutenant. The trio barely manages to leap off the platform before it crashes. Now grounded, Kay forces the spy to go his own way. Kaneda and she stumble across Akira's chamber. Meanwhile, the spy corners Ryu's lieutenant on an elevator platform. Suddenly, intense cold from Akira's chamber consumes the site meaning Akira is dangerously close to consciousness. The Colonel orders his troops to retreat. As Tetsuo reaches Akira's resting place, the cryogenic chamber begins to crack from within.
AKIRA--a small sleepy child awakens from a thirty-eight year long sleep. He stumbles hesitantly to the person who woke him--Tetsuo. From the chamber that has held Akira a deadly cold wave rushes forth flooding tunnels around the site. The cold extinguishes the life from all it touches, but it is only fitting justice for its victims are the ones who have helped keep Akira asleep...entombed...stealing a part of his life. Akira stumbles away from his almost tomb, seeking only the lovely warmth, following Tetsuo up to the bright blinding light of the sun. Across Neo-Tokyo the civilian defense claxon sounds, people scrambling for shelter. What do they fear? It is only a child waking from a nap...