Tokyo, as we know it, was destroyed by a kind of a new super-bomb of unknown origin. 9 hours after, World War III broke out and most of the major cities in the world were completely destroyed. 31 years after, Neo-Tokyo now stands, were the old Tokyo once was.

One night, Kaneda and his motorcycle gang are riding through the Neo-Tokyo Slums, and on of their members have an accident with a little boy with a wrinkled face, as one of an old man. Tetsuo crashes into the boy (who mysteriously remains unhurt and then simply vanishes from sight).

Tetsuo is brought to Hospital, and everything seems to have normalized. But that is not at all the case:

The strange boy was a part of a secret military project dealing with supernatural powers. The project is lead by the "Colonel", who wants to develop human weapons with aid of these powers. On his trail are Ryu and Kei (not Kay), members of a semi-terroristic group, who want to discover and destroy his plans.

And now Tetsuo is going to be a new member of the project. But his powers rise much faster than the Colonel or anyone else involved in the project has expected. Tetsuo escapes from his captors, killing possibly hundreds of highly trained mitlita, and manages to find out the location of an underground freeze chamber, where the mysterious AKIRA is kept.

Akira, too was a member of the project. But why did they put him in the freeze chamber at 0,0005 Kelvin ? They were afraid of something. Something they couldn't control anymore. Something Tetsuo is going to set free really soon . . .

And in midst of all the trouble: Kaneda and Kei.