As our heroes and Team Rocket beat the odds by surviving the sinking ship, they are dragged into another potentially deadly situation when they are attacked by the ferocious Pokémon, Gyarados. One Gyarados becomes many and Ash, friends and foe are swept up in a tornado landing them in various locations on an island. Ash loses Pikachu and the Poké Balls containing Charmander, Squirtle and Bulbasaur. Jessie and James from Team Rocket, who land in another remote part of the island, also lose their Pokémon. Thus both Pokémon and their masters are left searching for each other on this strange island, inhabited by gigantic Pokémon. Where could this island be?

After the attack caused by a group of Gyarados in the last episode, Ash and his friends end up on an island, where they realize that four of Ash's Pokémon, including Pikachu, are missing. On another side of the island, Jessie and James are awakened by a Krabby to find their Pokémon, including Meowth, are missing. They try to call for help in a phone booth, but they soon remember they don't have any money. On another part of the island, a separated Pikachu finds the Poké Balls of the separated Pokémon and releases Bulbasaur, Charmander, and Squirtle. They then see a Slowpoke fishing in the sea with its tail. Pikachu and Charmander decide to ask for help but with little result while Bulbasaur and Squirtle relax on the beach.

While trying to find Ash and the others, Ash's Pokémon are found by Team Rocket's Pokémon, Koffing, Ekans and Meowth. Meowth tells Koffing and Ekans to attack Ash's Pokémon, only to find out they won't battle for him because he is not their master. They also tell him that they are not bad guys and only take bad orders from their masters, much to Meowth's dismay, leaving him unable to battle Ash's Pokémon. Each side tells the other about their missing Trainers and Koffing and Ekans get visibly upset when Bulbasaur mentions that their Trainers may have abandoned them. Pikachu immediately refutes the very idea, telling Bulbasaur that Ash would never do something like that. The two sets of Pokémon join together to find their Trainers. Meanwhile, Meowth is tied up for what he has done to Pikachu and the others in the past. While they are eating, a giant Rhydon frightens them. The Pokémon escape, accidentally leaving Meowth tied up. Pikachu unties Meowth so he can escape. Meowth shows no gratitude for Pikachu's action, instead pushing him and saying that he could have got out himself. At the same time, Ash, Misty and Brock are being chased by a giant Zapdos. They soon elude it and decide to rest for the night. Ash vows to find his Pokémon no matter what. Meanwhile, Jessie and James are being chased by a huge Moltres. They run into a sign and are both knocked out, causing them to escape the Moltres.

The next day, Team Rocket runs back to the phone booth and Jessie makes a phone call. When James tells her that they don't have money, she says they are calling the boss by collect. They annoy him with their motto, causing him to hang up on them. Jessie and James then use a wire to get help by pulling on it while inside, hoping it will lead to the phone company. They see a Pikachu and decide to catch it, not realizing until it is too late that it is in fact a giant Pikachu. At the same time, Ash and company run behind a rock after being attacked by a giant Charizard. Meanwhile, the Pokémon, still searching for Ash and Team Rocket (and having agreed to a truce until they find them), come across a giant Blastoise. Squirtle is forced to ask it for directions by the other Pokémon, something that it's not too happy to do. Squirtle tries to start up a conversation with the giant Blastoise but it gets attacked by its Hydro Pump. They then see a Venusaur and Squirtle this time asks Bulbasaur to seek help from it as Squirtle thinks it's one of Bulbasaur's relatives. Bulbasaur is too afraid to ask the giant Venusaur and so says that it's an orphan and has no family, to which Squirtle decides to call it a "coward." Team Rocket, still pulling the telephone wire, are now being chased by a huge Kabutops. They decide to jump into a rail cart to get away. It starts moving but begins to head backwards toward the Kabutops, rather than away from it. It gets its foot tied in the wire and is dragged after Team Rocket. Then Ash and friends find the giant Pikachu, which is then knocked down because of Team Rocket and the trailing wire on the rail cart. Ash and friends fall into the cart with Team Rocket inside. Then they see their Pokémon chased by a giant Charizard, Blastoise and Venusaur. The Pokémon manage to jump to their Trainers and are at last reunited. Then the cart is sent flying into the air because of a giant loop in the rail tracks causing them to fly and crash into the giant Zapdos which they then discover to be robotic. Soon all the other giant robot Pokémon crash into each other and lie broken in a massive pile on the beach. Then the rail cart crashes into the water. A Gyarados shaped boat approaches the island. Inside, a woman introduces what appears to be tourists on the boat to Pokémon Island, however on noticing the damaged Pokémon, apologizes and then makes a call. It is revealed that the island is actually an attraction park owned by Team Rocket's boss, Giovanni, who isn't too happy with the destruction of Pokémon Land.

Ash and his friends continue on, ending up in Porta Vista. Meanwhile, the Slowpoke from earlier in the episode is still sitting on the rocks. It stands up, revealing a Shellder attached to its tail. The newly evolved Slowbro looks forward and says its name proudly.