Tommy had a Mudkip, whom he trained a lot. The two of them were friends, even after Mudkip evolved into a Marshtomp. Tommy went on a ship, which crashed. Tommy was forced to leave and forgot Marshtomp on the ship. During the time on the ship, Marshtomp evolved into a Swampert, but also started to distrust humans.
While Tommy was searching for Marshtomp, Swampert opened the door; Torchic went in and was startled by Swampert, who took it away. The heroes and Tommy went to search for Torchic, but May and Max, as well as Team Rocket, were taken away as well. Brock sent Mudkip, who followed the monster to a room, where May, Max and Team Rocket were captured. Tommy saw the monster was a Swampert, who started to attack them with Mud Shot. Ash sent Corphish to use Crabhammer, but was quickly defeated by Swampert's Iron Tail attack. Tommy knew the Swampert was actually his Marshtomp, who evolved during his absence. Swampert was hostile, but Tommy managed to calm it down, after Swampert saw Brock's Mudkip and recalled its happy moments with Tommy. Everyone was released from their capture, though Team Rocket went to capture all the Pokémon. Tommy had Swampert blast them off with Hydro Pump. Later on, Swampert was seen on the boat with Tommy, who took the heroes to Slateport City.