While being transported to the Iga village, the secret princess Kirihime is kidnapped by the evil Yoshiro Yukikusa, commander of an evil demon army. Kage and Chihiro are ninjas from the Iga village, and are sworn by their loyalty to do all they can to rescue her. They must face Yoshiro's endless demon ninja army on their quest across Japan.
As ninjas, Kage and Chihiro make use of a variety of ninja equipment and abilities. Kage uses katana and shuriken, while Chihiro uses a kusarigama (a chain with a blade on the end). Between stages, the player can arrange orbs they've collected on a grid to create different ninjutsu, or ninja magic. These have a variety of uses, including elemental attacks, damage reduction, and quicker attacks. New skills are also regularly learned, such as combination moves and new attacks, as well as increased jump height (in keeping with the absurd jumps the original game is known for).
After clearing the game, a hard mode is unlocked. There is also an art gallery featuring production illustrations, unlocked by meeting various conditions in the game.