Set sometime during the 21st century, the player controls the grandson of the ninja master Joe Musashi, also named Joe, who is on a mission to defeat the minions of Cyber-Zeed, a terrorist organization founded by the remnants of the Zeed organization that the original Joe Musashi destroyed. Joe must fight his way through a series of six stages in order to prevent Cyber-Zeed from launching its stolen stockpiles of plutonium around the world. The stages consists of a construction site, a harbor, a heliport, a jungle, a waterfall, and the hideout of the enemy.