An Egg belonging to the Mythical Pokémon Manaphy is found floating in the sea by mercenary Phantom the Pirate, but it is subsequently stolen back from him by Jack “Jackie” Walker, a Pokémon Ranger disguised as one of Phantom’s crew members. Walker joins the Marina Group, a traveling circus family that specializes in Water-types, to deliver the Manaphy Egg to Samiya, an undersea palace built by the People of the Water, whom the Marina Group are descendants of. Pokémon Trainer Ash Ketchum, his Pikachu, and their friends Brock, May, and Max become lost on their journey and encounter the Marina Group in their search for water, inadvertently becoming involved with Walker’s mission.
When Phantom leads an assault after the Egg, Manaphy hatches in May’s arms, who presumes she is its mother. The group eventually escapes Phantom by running into a network of ruins belonging to the People of the Water, where Ash and his friends learn about Samiya. Walker declines Ash and his friends’ further involvement with his mission and departs in a boat with the Marina Group toward Samiya. However, Manaphy shows discomfort and starts crying without May’s presence, forcing Ash and his friends along anyway. Manaphy’s natural instincts lead the boat toward Samiya, and to Walker’s dismay, May and Manaphy bond closer. Walker requests that Ash helps him separate the two, but May overhears them and becomes heartbroken over her and Manaphy’s inevitable farewell. One day, May loses her bandanna to the wind and Manaphy embarks far into the ocean to retrieve it. Lizabeth, the Marina Group’s daughter, along with Ash and his friends, board a submarine to search for Manaphy, eventually finding it along with Samiya during the expected lunar eclipse. Unbeknownst to them, Phantom had been in pursuit the whole time.