The Cyber Shinobi is the SEGA Master System exclusive sequel to Shinobi. In some context the game has the subtitle Shinobi Part 2. It was the first Shinobi game to not have an Arcade counterpart.

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.