Phantom the Pirate commands a crew obsessed with seizing the Sea Crown to conquer the Temple of the Sea, Samiya. Equipped with a powerful mechanized suit and a submarine base armed with supersonic projectors designed to inflict pain on Water-type Pokémon, he targets the Mythical Pokémon Manaphy, the "Prince of the Sea," to locate Samiya.

His quest begins by stealing Manaphy's egg, only to lose it to Pokémon Ranger Jack Walker. Phantom relentlessly pursues Walker, Ash Ketchum, and their companions to reclaim the egg. Upon infiltrating Samiya, he removes crystals from the Sea Crown, triggering the temple's destabilization and imminent sinking. Though he briefly escapes capture, Phantom later kidnaps Manaphy, only to be foiled by Ash empowered by the Sea Crown.

In his final stand, Phantom attacks using his submarine's supersonic projectors. Manaphy retaliates by summoning a legion of Water-type Pokémon, including Kyogre, which destroys the vessel. As the submarine collapses, Phantom's mechanized suit malfunctions while he struggles to hold up falling debris, leading directly to his defeat and capture. Post-credits scenes confirm his imprisonment alongside his first mate, Galen.