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.

Just as Ash and friends arrive at a new island, their ears are met with cries for help. A family had built their house upon a Corsola nesting ground, and when a new, hyperactive Corsola arrived and frightened off the previous Corsola residents, the ground beneath the house weakened and the house was washed out to sea. The father and daughter who had been outside during the catastrophe now look on helplessly as another daughter-trapped inside the house-is washed out toward a large whirlpool. Ash and Misty call their Pokémon to action and manage to save the young girl, but this proves to be only the first challenge of the day. As Ash and friends set about recollecting the Corsola that had reinforced the foundation of this family's home, Team Rocket soon arrives and attempts to steal not only the needed Corsola, but also collections of local artwork made from Corsola horns, which these Pokémon shed regularly. While assisting this local family, Misty waits not so patiently for an opportunity to catch the Corsola that had first driven the others away, and make it her own.

Ash and co. go after a treasure chest in a sunken ship.

After reaching the town where the preliminary round of the Whirl Cup is held, Ash and Misty enter and earn the two victories required to continue on to the finals. A friend they had met earlier is not as fortunate. When Misty tries to console him with promises of the next Whirl Cup to be held in three years, he remains depressed, saying that it was not lack of ability but the low spirits of his Octillery that had brought about his defeat. The Pokémon had been depressed ever since it evolved from a Remoraid and was subsequently spurned by its onetime Remoraid friends. If the boy cannot somehow mend these friendships between Pokémon that have now grown different in appearance, he doesn't see any hopes of victory even in three years time. Ash and friends willingly lend their knowledge and enthusiasm to this problem of Pokémon sociology.