Ace female test pilot Kusomoto Elle humiliates macho tank driver Lt. Kilgore in the first demonstration of the advanced personal battle tank, the MADOX. Kilgore vows revenge, and gets his chance when the army rather carelessly loses the prototype in Tokyo. The MADOX is found by engineering student Sujimoto Kouji, who doesn't take the time to completely read the manual and ends up zooming around Tokyo trapped in a machine he doesn't quite know how to operate. Guess who gets the job of stopping the now mobile missing MADOX? Poor Kouji. If he's late for his date, it's over between him and his girlfriend. His current attire redefines the term "over-dressed." And to top it all off, Kilgore wants to make him late- as in "the late Kouji!"

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.