Legend of the Mystical Ninja follows two main characters, Goemon and Ebisu-Maru, as they embark on an adventure to save their village from evil spirits that have taken control of the other villagers. Their journey takes them across Japan, through various locations such as mountain villages, amusement parks, and castle fortresses.
Legend of the Mystical Ninja is an action-adventure game where players control either Goemon or Ebisu-Maru, with the option to play in 2-player mode. The gameplay involves exploring village-type levels, side-scrolling jump and run stages, and participating in various mini-games that can earn money and items. Players must also navigate obstacle-filled "action areas" at the end of each village, where they can use special attacks and ride piggy-back on each other to overcome challenges.