Years after the events of Megazone 23 II, the only city on Earth is the supposedly idyllic Eden. There lives Eiji Takanaka, a B Level hacker who has just been accepted into EX, the organization that controls Eden. However, before his first day on the job, he becomes embroiled in a network war, a legendary figure named EVE, and a plot to re-inhabit the Earth.

It's the 22nd century and Shambhala city reporter Youko and her android boyfriend, bodyguard and cameraman Pete are hunting the enigmatic criminal Mr. X. Their search leads them to the Rainbow Tower, were Youko is taken hostage and Vito must battle to save her by destroying the program of the Tower's central computer to prevent X's escape.

Student Tako is inexorably drawn toward Sao despite class rumors that she has appeared in a porno movie.