The kids are heading to Maisie Island on a ferry when they spot a Spoink floating on a log. They quickly realize it's the same Spoink they helped before. When they save it and bring it aboard, it trips, dropping its pearl overboard. Ash's Pokémon go looking for the pearl with no luck.
When they arrive on the island, they meet a scientist named Isaiah who is doing research on Clamperl and their pearls—which end up as Spoink pearls. The jewel of his collection is a rare blue pearl.
Team Rocket sneaks in and tries to steal the blue pearl, only to be beaten out by Spoink stealing it first. Everyone goes looking for the little Psychic-type Pokémon. Meanwhile, the blue pearl accidentally gets switched with the pink pearl from a wild Clamperl. When this fact is discovered, everyone goes looking for the Clamperl and Team Rocket steals it away.
Team Rocket is trying to get the Clamperl open when the kids catch up to them. Spoink protects the Clamperl, who uses Water Gun to send the thieves blasting off. The Clamperl returns the blue pearl to Isaiah, and in exchange for the Psychic-type Pokémon's help, gives its pink pearl to Spoink.