Ash and his friends, after having won the Gym battle, try and board the last ferry leaving off Cinnabar Island. As Ash runs, he crashes into a Wartortle which unexpectedly appeared in his path. Ash checks Wartortle's data on his Pokédex, as Wartortle tries to signal to Ash and his friends. Pikachu understands his pleas and releases Ash's Squirtle from its Poké Ball. After talking with one another, Squirtle procures a pair of Squirtle Squad Sunglasses from inside his shell. Much to their surprise, Squirtle and Wartortle dive into the ocean, prompting Ash and his friends to take a boat and follow them.
Whilst following the two water Pokémon, Ash and his friends notice they are nearing an island. Ash realizes that the island is shaped like a Squirtle shell. Following behind them, Team Rocket is in close pursuit inside a Gyarados submarine. As they land on the island, the group come across several Squirtle and Wartortle shells, who appear to be sleeping. Perched upon a rock, Ash and his friends notice a large Blastoise shell towering over the other shells. Ash eagerly approaches it, but instantly falls into a deep slumber. The same fate befalls Squirtle. Brock and Misty try to wake Ash, to no avail. Misty tells Pikachu to electrocute Ash and Squirtle, thereby waking them up abruptly.
Ash reveals that he heard a sound coming from within the Blastoise shell, which caused him to fall asleep. Misty attempts to leave the island, but Ash refuses to give up, proclaiming that he will wake up the Blastoise. Ash and his friends commence "Operation Wakeup" with the assistance of the other Squirtle and Wartortle. Meanwhile, Team Rocket are eavesdropping on them, and state their aim to steal the sleeping Blastoise and the other turtle Pokémon. Brock recounts the history of the island, which was the Kingdom of the Turtle Pokémon, presided over by their leader, Blastoise. After Blastoise was recovered from the ocean, all of the others fell into a deep sleep. Wartortle ran to the mainland, when he met Ash.
After Brock attempts to check the Blastoise's vital signs, it begins to awaken, with Ash still on its back. There is revealed to be a Jigglypuff stuck inside one of Blastoise's cannons. It begins to sing, and they all fall asleep. Team Rocket choose this moment to reveal themselves, and attempt to capture Blastoise. As usual, Meowth is the one to go out, but he ends up falling prey to Jigglypuff's song. To prevent themselves from getting too close to Blastoise, they use their "Gyarados Grabber" to pull it into their submersible. Ash, Misty and Brock wake up abruptly, and realize that Blastoise is missing. Ash's Squirtle brings order to the other Pokémon, rallying their support.
They pursue Team Rocket after following the trail left behind by Blastoise. Team Rocket celebrate their successes, but squabble over who gets to lay claim on Blastoise. Meowth is knocked into the side of the submersible, dislodging Jigglypuff and causing several cracks in the structure. Jigglypuff's song begins to reverberate throughout the ship, as Team Rocket succumbs to its effects. JUst as this happens, their submersible begins to take on water, but before it can sink the Squirtle Squad brings it up to the surface. Ash and his friends resuscitate Team Rocket, who deny ever asking for their assistance.
They flee back to their submersible, which transforms into a Mecha Gyarados. The giant machine charges straight at Blastoise, to which the Squirtle Squad attempt to stop it with their Water Gun attacks, to no avail. The Mecha Gyarados proceeds to chase the Squirtle Squad, as Ash calls out to the sleeping Blastoise. Squirtle and Pikachu use their signature attacks in conjunction with one another, which expels Jigglypuff as Blastoise awakens. Blastoise manages to stop the rampaging Mecha Gyarados with brute strength. Despite Team Rocket's best efforts, Blastoise and the Squirtle Squad send Team Rocket blasting off again.
Jigglypuff emerges inside the Mecha Gyarados, and begins to sing its song. Team Rocket falls asleep, as their machine falls into the ocean. Ash's Squirtle jumps in after them, attempting to rescue Jigglypuff. After a few tense moments, Squirtle emerges with Jigglypuff, who resumes its singing. This sends everyone into a deep slumber once more. Enraged, Jigglypuff squiggles on everyone's faces with its marker. After having resolved the conflict, Ash and his friends leave the island in peace, heading off to get his 8th Gym Badge. Meanwhile, Team Rocket are floating in the middle of the ocean. After Jessie and James proclaim that they are getting sick of losing, Meowth exclaims that he is getting seasick.
- The Squirtle Squad leader sunglasses from Here Comes the Squirtle Squad return.
- "Pokasso" as Brock called Jigglypuff was a parody of the famous french artist Pablo Picasso.
- Squirtle appear in this episode, wearing sunglasses.
- The "Who's that Pokémon?" in this episode is Horsea.