Goemon and Ebisu-Maru are enjoying themselves at home when they hear about strange spirits spotted at the Legend of the Mystical Ninja temple and taking control of other villagers. Concerned, the two set out to confront it at the temple, which marks the beginning of a new adventure that will take them across Japan.
Players control either Goemon or his partner Ebisu-Maru (or both in 2-player mode) as they travel through villages and side-scrolling action stages. In the overhead-view villages, enemies must be defeated to earn money and other items. Players can attack with their primary weapon, jump, and throw weapons, which consume money each time used. Attacking innocent villagers will result in losing money.
Players can also visit various businesses such as shops, restaurants, inns, and the judo training center to gain money or lose it. Visiting houses often features mini-games like mazes, whack-a-mole, lottery, dice, a 3D labyrinth, and a trivia quiz show. Each village ends with an "action area" that changes the game into a complete side-scroller filled with obstacles, traps, enemies, and bosses.
Characters can also use special attacks, which consume scrolls collected beforehand at the judo training center. In 2-player mode, characters can ride piggy-back on each other to avoid getting stuck by scrolling screens.