Cyber Shinobi is a one-player game that takes place in a world threatened by an evil force known as "Cyber Zeed". The story begins with the escape of some villains from the previous game, which sets off a chain of events leading to the attack on atomic power plants around the world. Plutonium, equivalent to 100,000 megatons of explosive power, is stolen, and Cyber Zeed's plan to use it to terrorize the world becomes clear.
Players take on the role of Joe Musashi, who must fight against ninjas that rise from the ashes in six rounds. The gameplay involves using fists and legs to defeat enemies, as well as utilizing special attacks and ninjitsu. Power-ups can be collected along the way, granting more shots, ninjitsu, power, and life. Each round culminates in a boss battle, which must be defeated to progress.