Masato, May's younger brother, travels with Ash Ketchum, May, and Brock. He joins the mission to protect Manaphy, the Prince of the Sea, after meeting the Water-type Pokémon specialists of the Marina Group circus family and Pokémon Ranger Jack Walker. Masato helps the group flee Phantom the Pirate, a mercenary hunting Manaphy for its ability to find the undersea palace Samiya.

During Phantom's attack, Masato escapes with the others through ancient ruins connected to the People of the Water, descendants of Samiya's builders. He later boards a boat with the Marina Group and Ash's companions heading for Samiya, compelled to act after Manaphy's distress call separates it from May. Masato participates in the search for Manaphy when it dives to retrieve May's lost bandana, joining Lizabeth, Brock, and others in a submarine. This search leads them to discover Samiya during a lunar eclipse.

Inside Samiya, Masato witnesses Phantom steal the Sea Crown's jewels, an act that sets off flooding and causes the temple to sink. He escapes to the submarine with Lizabeth and Brock amid the chaos, becoming separated from Ash, May, and Manaphy. Masato observes the temple's resurgence and Manaphy's farewell from the submarine before continuing his journey alongside Ash, May, and Brock.