At the request of Impact, Goemon and his friends travel to several planets in order to defeat the evil commander Harakiri Seppukumaru. The game introduced the "Oni Oni Rendezvous" and title themes which would be used in later titles. The anime based on the series also uses some elements from this game, including the appearance of Seppukumaru and his followers.
Kirakira Dōchū returns to the map-based gaming of Ganbare Goemon 2 and the inclusion of mini-games. Each character is assigned a different world, with several side-scrolling levels and 1-2 towns. Each world has a castle stage, in which the boss fights consist of mini-games. The game also features voice-acting.