In a scuffle with Team Rocket, Ash and friends are thrown from the ship bearing 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 the children back to a ship wherein awaits their old friend, Professor Elm. They ride the ship to a bustling harbor in the first of the Whirl Islands. There they learn of an upcoming competition in which Water Pokémon trainers will vie for the title of Whirl Island champion.

Ash and friends discover an island on which the Pidgey population-long protected by environmental regulation and free from predators-has grown to unusually stout proportions and virtually abandoned any desire for flight. There Ash and friends find one Pidgey, however, in which the desire to soar through the heavens burns more fiercely than even in Pidgey from beyond this island. Anxious to see this Pidgey achieve its dreams, the young trainers join with the Pidgey's trainer and follow the Pokémon in a jet-assisted hot air balloon, tracking its flight as the Pidgey climbs higher into the stratosphere than any Pokémon in history.

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. Long ago seismological forces had combined to lift the mountain out of the depths of the sea, bringing along with it the undersea nesting ground of these Chinchou.