As with many action/platformer video games, the plot is minimal except for revealing future stages. In this game, the players control Goemon and Ebisumaru (called Kid Ying and Dr. Yang respectively in all non-Japanese releases). After noticing some odd occurrences in their hometown, Goemon and Ebisumaru decide to investigate. They soon discover that Princess Yuki has been kidnapped by the Otafu army. To save the princess, the protagonists must travel through different regions of Japan to find clues about the army and the location of the princess.