On their way to May's first contest in Slateport City, Ash and gang travel across the sea on a motorboat. After Team Rocket fails in their latest attempt to steal Ash's Pikachu, the boat stops working. Drifting along, they spot a large, abandoned ship and decide to go inside upon seeing a smaller boat off to the side.

Inside, they meet up with Tommy, a trainer who lost his Marshtomp on the ship long ago. He promises to give Ash and company a lift after he is done searching. Several Pokémon start to go missing and soon May, Max and Team Rocket are captured too. A Swampert and a Spinarak reveal themselves as the culprits.

Ash, Brock, Pikachu and Tommy soon come across the Swampert and Tommy recognizes the Swampert as his Marshtomp, but it retreats further into the ship. After saving the others, Tommy reunites with his lost friend and apologizes for leaving it behind. After thwarting another of Team Rocket's schemes, Ash and company leave on Tommy's boat for Slateport.