Goemon and his friends are facing off against the evil Skull King and his pirate army as they try to take over Ancient Japan. The group must navigate through various locations such as Gadget Castle, The Black Ship Skull, The Demon Cave, and Skeleton Island in order to reach the final showdown with the Skull King.
Mystical Ninja Starring Goemon is an overhead action game that combines elements of exploration and light RPG. Players can explore towns, dungeons, castles, and more, as well as shops and inns where they can rest and recover their strength. The game features challenging boss battles at the end of each level, but to defeat them, players must compete in a mini-game called "The Surprise Match", which often involves button-mashing or memory match-style gameplay.