The journey takes the ninja heroes from an amusement park to the top of a tower. Along the way, they must survive endless attacks from the members of Kage Ichizoku and their minions. The protagonists Joe and Hayabusa uses shurikens as their primary weapon, although other weapons that aid them along the way are nunchakus, maces, ratchets, battle axes, spiked clubs, and katana swords. A special somersault attack can be used to knock down a multiple enemies in a row. As an art of ninpo kairou, a fire dragon can be summoned to destroy all enemies on the screen.
The story, set in the year "199X", follows the twin ninja warriors named Joe and Hayabusa, who are waging a battle against an evil ninja clan Kage Ichizoku. Their mission is to fight their way into the enemy home fortress, the Ninja Tower, which has emerged from the ocean in the center of New York City, to once and for all defeat the Shadow Family and its leader, the long thought-dead demon sorcerer Genyousai. When defeated, three of the bosses: Musashi , Kagerow and Gembu, become allies and fight alongside Joe and Hayabusa as optional player characters. If the heroes are victorious, Genyousai is destroyed and the Ninja Tower crumbles.