In a scuffle with Team Rocket, Ash and friends are thrown from the ship that is brining them to the Whirl Islands. As powerful whirlpools draw them toward impending doom, a mysterious form under the sea shifts the powerful undertow, drawing them to safety. Shortly thereafter, a Corsola comes skipping over the sea's surface and guides them back to a ship where their old friend, Professor Elm waits. They ride the ship to a bustling harbor on Blue Point Isle. There they learn about an upcoming competition in which Water Pokemon trainers will battle for the title of Whirl Islands champion. Meanwhile, Team Rocket is planning on attacking the Pokemon Center so they can steal all of the Pokemon there.

On their way to the Whirl Cup competition, Ash and friends are fortunate enough to pass a small mountain village just as an annual Chinchou migration is about to occur. When both a vicious rainstorm and Team Rocket threaten the travel to the Chinchou's breeding grounds, Ash and friends must help Dayton and his father keep all the Chinchou safe.