The story is set in Nagasaki prefecture in Minami Shimabara city, the fabled origin of the Shimabara Rebellion that sent shockwaves through all of Japan in the early Edo period. It is also where a third-year junior high school student named Shirou spends his days with his school friends. One summer day, Shirou's older childhood friend Akane returns to Minami Shimabara from Tokyo. Shirou and Akane take a stroll around Minami Shimabara with another longtime friend, Tokiya. While these friends are dealing with nostalgia and more complex feelings, a mysterious creature named Goron suddenly appears before them. This encounter with a mere little creature causes great events to unfold once more in this city...

The Straw Hats visits an island, known as Mecha Island, where a fisherman sings an old folk song about a Golden Crown. Searching for that mysterious treasure, they find a hidden entrance into the island. The island's leader, Ratchet, impressed with the find and in search of the Golden Crown himself, invites the crew to join him in his search and the crew along with Ratchet and his henchmen enter the cave. As it turns out, the islands true form, is that of a giant turtle. Ratchet, who had known this all along, uses his mechanical castle to take control of the turtle, in order to use it, to take over the world. Now the Straw Hats have to stop not only Ratchet, but also the helpless turtle, from crashing into a nearby island.