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.
While the group sail towards their next stop, Maisie Island, Pikachu and Torkoal notice a Spoink out at sea. After a freak wave crashes over it, the group stops and pulls it aboard, quickly realizing it is the same Spoink they met before. It hops around happily due to the rescue, but trips over the life preserver, and its pearl goes flying out into the water. Spoink is initially saddened by this, but it notices a round buoy on the boat, which it promptly places on its head. Ash grabs the device, saying that it doesn't belong to Spoink, and Torkoal cries at Spoink's situation. Torkoal then impulsively jumps into the water, intending to look for Spoink's pearl. Worried that the Fire-type will be seriously hurt from being underwater so long, Ash dives in after it and rescues it. Instead, Brock and Ash send out Mudkip, Lombre and Corphish, respectively, to try to find Spoink's pearl. However, they find no sign of the pearl, and report back to the group empty-handed.
During a quick rest-stop at Maisie Island, the group wonders what they can do to help Spoink. A young boy and his Azurill run by, and Spoink tries putting Azurill on its head. The boy cries, and Ash and Brock snatch Azurill away, scolding Spoink. Spoink then tries on many other round objects, including a Swablu, a Castform, and even a large Wailmer. In the end, however, it is still disappointed at its pearl-less head. A scientist named Isaiah approaches the group and explains that the pearls grown inside a Clamperl are the same kind of pearl that Spoink wear. He escorts Ash and his friends to his lab, where they find a pool enclosure with large rock formations in the middle; a group of Clamperl are on the rocks. May comments on how cute they are, and scans them with her Pokédex. While Isaiah further explains the connection between Spoink and Clamperl, Spoink becomes excited over a blue pearl in a display case. The group admires it, and Isaiah admits that it is a rare find while Spoink stares at the pearl sadly.
Now aware of that pearls are created by Clamperl, the group begin their search for one. As a young girl and her Shroomish run along the beach, Spoink puts Shroomish on its head psychically, though May snatches it away, while Ash and Brock scold Spoink again. May returns Shroomish to its Trainer, apologizing, but the two promptly run away. They then realize that Spoink is missing. Meanwhile, Team Rocket sneak into the museum, intending to steal the valuable blue pearl. James removes the display case, but before Jessie can grab the pearl, Spoink hops by and psychically puts it on its head, hopping all the way out the window. A security alarm alerts the group to something amiss at the Clamperl lab, and when they arrive they are greeted by Team Rocket disguised as janitors who reveal that Spoink took the blue pearl. The trio “get back to work” while Ash and May send out Swellow and Beautifly, respectively, to search from the air. Everyone else splits up and searches on the ground. Looking on, Team Rocket sets their sights on Spoink and the blue pearl, planning to give both to Giovanni.
Spoink happily hops along the beach with its new pearl when it encounters the two kids from earlier. They hold their Pokémon away from Spoink, afraid of what happened before, but then they realize it has a pearl now. However, Spoink slips again, and its blue pearl flies off. It ricochets among the rocks, lands inside a sleeping Clamperl, and knocks Clamperl's pink pearl out. The pink pearl somehow ricochets its way back to Spoink's head. Spoink is happy and bounds off, and the kids wonder why it had that blue pearl in the first place. Beautifly reports back to the group that it had found Spoink, and leads them to it. They notice with surprise that Spoink is now wearing a pink pearl again. The two kids approach, and directs the group to the wild Clamperl's location, where the pearl swap occurred. The group thanks the young Trainers and make their way over. Spoink and the others find the Clamperl, but it now has its shell closed. The Clamperl soon opens its shell to reveal that it does indeed have the blue pearl. May asks if they could have the pearl back, but Clamperl refuses. Spoink then takes the pink pearl off its head and offers Clamperl a trade; it agrees, and May thanks it. Before they could make the switch, Team Rocket drops a smoke bomb and says their motto.
Jessie sends out Seviper, and Ash counters with Torkoal. Seviper lunges in for a Bite, and the attack proves too quick for a counterattack, so Ash tells Torkoal to use Iron Defense. Seviper ends up hitting its head on Torkoal's hardened shell. Ash then orders a Flamethrower, which Seviper dodges. Excited, since the battle is going her way for once, Jessie orders a Haze. Everyone runs around in confusion, but Team Rocket manages to meet up, with James carrying a sack containing Clamperl, and they escape in their balloon. When the smoke clears, the group realizes that Spoink and its pink pearl are still there, but Clamperl is missing. Meanwhile, Team Rocket has landed some distance away, and are now trying to entice Clamperl to open its shell to retrieve the pearl. Jessie sweetly asks it to open up, but it clamps shut before she can grab the pearl. James tries to physically pry the shell open, but that doesn't work either. Meowth then suggests they try tickling it, and the strategy leads Clamperl to partially opens up. Meowth taunts it with its tail to get it to open more, but Clamperl instead Clamps down on it. It then finally opens it shell, and Meowth's momentum sends it flying into a tree. The shell closes again before Jessie can grab the pearl. James then thinks that Chimecho's sweet voice and chiming may get Clamperl in a better mood, so he sends it out, but Chimecho's attempt fails as well. Jessie tries again, but this time, she is blasted into a tree by Clamperl's Water Gun. As Jessie becomes agitated and resorts to trying to wrench open the shell, Swellow spots them from above and reports back to Ash and the others.
Isaiah and the group arrive, with Spoink using Psychic to lift Team Rocket away from Clamperl and throw them at their balloon. The group checks on Clamperl, as Jessie and James send out Dustox and Cacnea. After Ash sends out Grovyle, Jessie orders a Tackle, and Grovyle counters with Quick Attack. Cacnea attacks Clamperl with Pin Missile, but Spoink jumps in front of it and uses Psychic to stop the pins. Grovyle hits Dustox with Bullet Seed, while Spoink fires a Psybeam at Cacnea. Clamperl slowly opens up as it watches its friends defend it. Dustox aims a Poison Sting at Grovyle, who dodges with a series of back-flips. Grovyle follows up with a Leaf Blade and scores a direct hit on Dustox. James orders a Needle Arm and Cacnea rushes forward, but Spoink sends it back with another Psybeam. Finally, a Water Gun from Clamperl blasts Team Rocket off.
Spoink and Clamperl are now free to carry out their previously arranged trade, and Spoink uses Psychic to switch the pearls. Isaiah thanks Clamperl, but Spoink is saddened to be without a pearl once again. Clamperl generously offers to give Spoink its pink pearl as thanks, and Spoink happily accepts.