After rescuing Princess Yuki and saving Edo, Goemon and Ebisumaru decided to take a vacation at the Ryūkyū Resort when suddenly Sasuke appears and tells them that Japan is being threatened by the Western general McGuiness, who along with his army of bunny men, tries to westernize Japan. Goemon, Ebisumaru and Sasuke head to bunny castle to stop McGuiness. As the trio chase him and his bunny men around japan, McGuiness schemes a plan where he kidnaps several non-playable character.