The game takes place during Japan's Edo period around the year 1630 in the province of Ohkami in the western region, where power has been seized by the evil tyrant Gyokuro. The player's goal is to end his oppressive rule and restore peace to the province.

The Ninja,originally released as Ninja Princess in Japan, is a run-and-gun game where the player shoots enemies and defeats bosses along the way. Enemies include samurai, ninja, and dogs. The player’s standard weapon is unlimited throwing knives, but power-ups for shurikens are available. Additionally, the player can turn invisible for a short time. Most stages scroll vertically, but some levels vary the gameplay, such as one where the player must scale a wall.