Phantom the Pirate is the main antaganist in the movie "Pokémon Ranger and the Temple of the Sea". At the beginning of the movie, Phantom managed to snatch the Manaphy Egg that is drifting through the sea and has it in his possesion for a few seconds until Pokémon Ranger Jack Walker steals it and escapes on a Mantine. The reason Phantom wants Manaphy is because he wants to become the "King of the Sea" but he can't become that unless the "Prince of the Sea" Manaphy shows him where the Sea Temple is.
Later he is seen tracking Jack and his friends. When he finds them, he and his crew attack them with Beedrills, but the gang escapes to the ruins left by The People of The Water in which Phantom follows.
Later at the Sea Temple, he is seen pulling crystals out of the Sea Crown (after following Jack, Ash and friends who were led by a now hatched Manaphy) one by one, causing the Sea Temple to start to sink and then escapes. Jack puts most the crystals back in place until the final crystal fell off the edge. Ash went to get it, nearly drowning in progress, and puts it back in the Sea Crown, stoping the Temple from sinking.
A while after that, he got out of the sinking temple on a water rocket. After the temple was saved, he came up and stole Manaphy one last time. However, Ash grabbed it back (in a yellow energy beam, now being the temporary "King of the Sea") and Phantom was flung into the water. This wasn't the end of Phantom, as he soon rose above the waves in his submarine base and attempted an onslaught using the base's supersonic projectors that caused all Pokémon in the vicinity to writhe in pain.
Manaphy, however, began to fight the sonic waves and counters with its Heart Swap ability, restoring order to the water Pokémon. Soon the water Pokémon counterattack the base, with the Wailord bashing the submarine (nearly knocking Phantom off in the process), as well as creating a tear in the base. The Chinchou swim into the crack, short-circuiting the submarine. Lastly, Manaphy ordered Kyogre to use its Hyper Beam to destroy the sub. On the remains of the sub, Phantom attempted to hold up a pillar of debris up to prevent it from crushing him, revealing his mechanized super-suit (the object of his overwhelming strength), in which Jack says "I didn't think he took his vitamins.". But after the suit malfunctions, the pillar crushes him beneath its weight.
During the credits, both Phantom and his second-in-command Galen are seen in prison.