The Phantom is a captain of a crew whose main goal is to posses the Sea Crown. Due to a mechanized suit he has super-human strength. He has vast knowledge about the People of the Water and even has a crystal from them. He travels around in a submarine and helicopter.
After finding a Manaphy egg, it was taken by Jack Walker. When Team Rocket saw the egg they called Phantom to let him know where it is. This led to Ash, his friends and the marina group to be attacked by him. When they escaped, Phantom followed them into the ruins with a crystal from the people of the water.
When Ash, his friends and the marina group venture towards Samiya, The Phantom was tracking them down, but was unseen by the group. When he reached the Sea Crown, he began stealing jewels from it, which caused the temple to sink. Jackie then came and put a few of them back.
The Phantom then got out of the temple on a water rocket. After Ash saved the temple, he came up and stole Manaphy, in hopes he can find the Sea Crown again. But, Ash infused with crowns power save it. But, Phantom then tried using his submarine to plan an onslaught. He used supersonic projectors to drive all the water pokemon in pain.
But then Manaphy led all the water pokemon to attacked Phantom's submarine. Then with a hyper beam from Kyogre destroyed it. Phantom tried to hold up his the debris but was crushed by them. He and his first mate Galen are then arrested afterwards.
In the movie, it appeared as though he had super strength, but by the end it was revealed that he was using robotic enhancements, similar to those used by A.J. and his Sandshrew.