Ash and his friends board a fancy cruise ship called the St. Anne, thanks to tickets provided by two friendly but familiar-looking people. We soon learn that they're actually Jessie and James in disguise, and their latest plan is to lure Pokémon Trainers onto the ship and steal their Pokémon!

While onboard, Ash observes a Raticate defeating a Starmie. Ash challenges the Raticate with his Butterfree. Though the Raticate's owner removes his Pokémon before the battle ends, he's impressed with Ash's Butterfree and offers a trade. Ash trades his Butterfree for the Raticate, but soon regrets his decision. Meanwhile, James is tricked into buying a Magikarp.

While all the Trainers are gathered in a room, the ship's employees reveal themselves to be members of Team Rocket! As they suck up Poké Balls with vacuum-like devices, the Trainers fight back; their Pokémon team up to multiply their attacks and drive back the bad guys.

During all the commotion, a tumultuous storm brews outside. Eventually, the ship rocks violently, and the consensus is to abandon ship. Only Jessie, James, Meowth, and Ash and his friends are unable to flee, as they are knocked unconscious by the jerking movements of the ship—then the ship flips over and sinks!

What will become of our heroes? Will they have to join forces with Team Rocket to escape? And how successful could such a partnership be?