New York is being overrun with crime, and the city's children are mysteriously disappearing. It is up to the Black Manta to rescue the children and stop whomever is behind this. In addition to his ninja skills, Black Manta will be able to acquire additional powers (including invisibility and teleportation) to help him out against the numerous and well-armed villains.

Wrath of the Black Manta is a side-scrolling arcade-style action game with five different levels. Throughout each level the player may come across various clues to help him find where to go next, or discover a hidden location. Some of the bad guys Black Manta comes across may also possess useful knowledge and can be interrogated if they don't kill him first.