In the game, the player goes through five levels, using throwing stars and special ninjutsu abilities called the "ninja arts", to stop a gang and the evil mastermind behind a slew of kidnappings, El Toro. One of the kidnapped is a student of the Black Manta's sensei, Taro.
The Black Manta has many powers, which he gets after beating a level. The player can choose which power to use by pressing start. These powers can help the Black Manta defeat enemies and bosses more quickly. The Black Manta can save kidnapped children hidden throughout each level, however, it plays no role in completing the game and does not warrant any kind of special bonus.
Part of the last level is seen through a first person perspective. Towards the end of this stage, the Black Manta has to defeat one of the bosses from the previous levels before he goes face-to-face with El Toro himself.