The player controls the modern-day ninja Joe Musashi, protagonist of previous Shinobi games, as he goes on a mission to rescue four kidnapped comrades from an enemy, gaining control of the other ninjas (each with different abilities) as the game progresses in a manner similar to Mega Man.

The Master of the Oboro school of shinobi sends his best students to investigate the suburban areas.

They return with news of a powerful dark force that has established a base within Neo City.

One by one his greatest pupils enter Neo City to locate and destroy the source of the evil.

As the oldest and strongest of his ninja disciples, Musashi must use his special skills in the art of ninjutsu to free his fellow shinobi.

The player starts the game as Joe Musashi (the red ninja), whose goal is to rescue four kidnapped allies who are being held captive in different stages.