After finding the Manaphy egg, it was taken by Jack Walker. Like any respectable pirate, The Phantom has a Chatot, a parrot Pokémon, and he uses this Chatot to closely follow Ash, his friends, and his new friends, Lizabeth and her family. After a battle with Ash imbued with the Sea Crown's power, he was trapped under some rubble until Jackie and the police arrested him.
Pirate used both his Pinsir and Parasect to stop Jack Walker from escaping.
Chatot was owned by The Phantom and followed him everywhere but later abandoned The Phantom in the sinking Sea Temple to be with Jack Walker. Chatot has a tendency to repeat everything The Phantom says.