Part 1: After his father's ship, the Kannonmaru sinks, Jiromaru decides not to take over his father's occupation and goes to Kyoto to become a samurai. However Jiromaru quickly realizes that being a samurai is not everything he had hoped it would be. He then hears rumor of the Kannonmaru appearing at various locations and tries to find out about this mysterious ship.

Part 2: The adventures of Jiromaru and his gang continue in their efforts to rescue Princess Yukihime and her servant Chacha from the pirates. All the while, Jiromaru is also in pursuit of the truth of the Ghost Ship; will he ever be able to unveil its mystery?