Ash and his friends are running to catch the last ferry off Cinnabar Island when they collide with a Wartortle. It tries to tell them something, but they do not understand. Pikachu taps one of Ash's Poké Balls and sends out his Squirtle, who begins to talk to Wartortle, in a serious and urgent manner. Suddenly, Squirtle gets a shocked look on its face, and pulls out its Squirtle Squad sunglasses, putting them on. Wartortle and Ash's Squirtle dive into the water and Misty's Pokémon tow the trio along in a boat. They lead them to an unnamed island that resembles a Squirtle's shell.
They find Wartortle and Squirtle inside their shells on the island, who upon closer inspection, Brock realizes that they are asleep. As they look farther up, there is a giant shell, which Ash's Pokédex reveals it is a Blastoise. Ash and Squirtle check out Blastoise, and suddenly they fall sleep. Misty and Brock try to wake him up, but to no avail. Then, Misty tells Pikachu to use an Electric attack, which manages to wake Ash and all of the Pokémon up. Misty and Brock asked Ash what happened, who then replies that when he approached Blastoise, he heard mysterious music that was vaguely familiar that caused him to fall asleep. Misty and Brock look at each other as if they recognize the cause, and Misty says that they should go ahead and leave, though Ash insists they should stay to help Blastoise. Misty, shaking her head and smiling, says that she was afraid of that.
Brock begins to tell the story from the Squirtle and Wartortle's point of view, with little pictures to illustrate it. It is revealed that the group live under Blastoise, who is considered their king. A few days ago, Blastoise was swimming in the ocean when it washed ashore. After retrieving Blastoise, the Squirtle and Wartortle also withdrew into their shells. He leads off by saying that when a Wartortle returned to find everyone inside their shells, it headed to the mainland to get help, and bumped into Ash and his friends. Misty comments that people have been searching for the Wartortle's breeding grounds for years, and that the island may be it.
Brock imagines that the discovery would be invaluable to learning about breeding. He puts on a doctor's outfit, and says that it is time for Blastoise's first annual physical. He pulls out a stethoscope but cannot hear anything. Suddenly, Blastoise's head and limbs pop out, lifting Ash into the air. He hops off, and then Blastoise's cannons pop out of its shell. Squirtle then notices something stuck in one of Blastoise's hydro cannons. It is revealed to be Jigglypuff, who starts to sing, and everyone falls asleep.
Later, Team Rocket intrudes on the island, hoping to catch Blastoise, but Meowth, the one who went to get Blastoise, falls asleep. Using the rope they attached to him, Jessie and James reel him back in, only to realize that he has fallen asleep. Jessie slaps Meowth to wake him up before tossing him aside. They then use their Gyarados grabber instead. With a press of a button, Team Rocket's Gyarados sub shoots out a suction cup, which sticks to Blastoise's shell. The Pokémon is reeled and clenched in the submarine's teeth.
Ash soon wakes up to discover that Blastoise has disappeared. He informs Misty and Brock, whilst the Turtle Pokémon are sent into distress. Squirtle's Water Gun helps to grab the attention of the other Squirtle and Wartortle before taking to a rock to calm them down. Ash takes credit for Squirtle's control of the situation, though Brock thinks it may just be the sunglasses. Pikachu suddenly notices the drag marks in the sand, and with that, the Squirtle and Wartortle dive one after the other into the ocean to search for Blastoise.
Team Rocket celebrates their successful escape over drinks, but they soon get into an argument over the credit for the capture. Jessie and James force Meowth out of the conflict, claiming that a Pokémon cannot own another Pokémon. James resorts to kicking Meowth away, though he hits the sub's wall, which disturbs Jigglypuff, and it also begins to fill with water. The unusual noise coming out of Blastoise's shell puts the trio to sleep as the sub begins to sink. Fortunately, the Squirtle and Wartortle arrive on the scene and bring the sub to the island.
Ash, Misty, and Pikachu help to revive Team Rocket from their near-drowning. They all open their eyes, though they soon realize they are surrounded by Ash and his friends, and James receives a clop to the head when he thanks Ash and his friends for saving them. Team Rocket retreats to their submarine after realizing they were surrounded. They sarcastically apologize before Meowth presses a button, and the Gyarados sub is transformed into a land vehicle armed with two claws. They chase the Squirtle and Wartortle around, while Ash's Squirtle and Pikachu try to wake up Blastoise. They succeed, and Jigglypuff emerges before flying into the Mecha Gyarados. Blastoise eventually wakes up, and with the other Turtle Pokémon's Water attacks, they successfully push Team Rocket out to sea.
Ash fears for Jigglypuff, who is still inside the mecha, and Squirtle goes to rescue it. An underwater explosion occurs, and Ash, Misty, and Brock fear the worst. A few moments pass before Squirtle emerges and returns to the island with Jigglypuff on its back. Jigglypuff starts singing, which puts everyone to sleep yet again. In another angry tirade, Jigglypuff scribbles on everyone's faces and the Turtle Pokémon's shells. Upon realizing this, everyone laughs off the incident except for Misty, who is annoyed because the marker scribbling makes her look like a cartoon character.
Later, Ash and his friends wave goodbye to the island and its Turtle Pokémon as they continue onward to Viridian City for Ash's next Gym match. Meanwhile, Team Rocket are miserable and trapped on the wrecked fin of their Mecha Gyarados, with Jigglypuff's marker scribbles still on their faces.