Seduced by the power offered to him, a samurai allows harm to come to his infant son. The son, fated to destroy the 48 Fiends, has 48 body parts removed, one by each demon. The samurai sets the remains adrift along a river, where the still-living child is discovered by a kindly doctor. After raising the child, the doctor operates on him, replacing his missing parts with mechanical ones. Knowing the child's destiny, the doctor replaces his missing arms with sword arms, attaches a repeating rifle to one arm, and a cannon to one leg. The game begins with the now-adult Hyakkimaru beginning his quest to reclaim his body parts from the Fiends. Soon joined by the child-thief Dororo, the pair embark on a quest against ancient Japanese demons and the monsters they create.