He lives on the Abandoned Ship, searching for his Marshtomp after he accidentally dropped its Poké Ball there many years ago. As it turned out, it evolved into a Swampert which attacked any intruders on the ship.
When the Swampert realized that Tommy was its rightful owner, it rejoined him and both Trainer and Pokémon were a team once again.
Tommy helped Ash and friends to get to Slateport City with his boat.