Ash and his friends wake up on the shores of a tropical island. They wonder how they possibly survive, and Ash notices that Pikachu, as well as three of his other Pokémon are missing. A little ways away, a Krabby pinches Team Rocket, waking them up. They too are amazed that they survived. Then they also realize that Meowth, Koffing, and Ekans are all missing. They notice a phone booth, but they can't make a call due to the fact that they have absolutely no money.
Soon after, on yet another part of the island, Pikachu wakes up, and, seeing Ash's three missing Pokémon, releases them. They are Charmander, Bulbasaur, and Squirtle. They'll all O.K., but they have no idea where they are. They see a Slowpoke sitting on rock and ask him where they are. The Slowpoke doesn't answer, and instead, sticks his tail into the water. They all then set off in search of Ash. As they walk along, they wonder what happened to Ash his friends. Squirtle suggests that maybe they got eaten by wild Pokémon, and Bulbasaur thinks that Ash abandoned them. They continue to talk and Meowth, Ekans, and Koffing show up. Meowth tries to attack them, but Ekans and Koffing refuse, saying that Meowth isn't their master. Meowth tries to tell them that they are all bad guys, but they disagree, saying that there is no such thing as bad Pokémon, just bad masters to make them do bad things. This stuns Meowth, as he thought he was bad all the time. Since Meowth can't fight Pikachu, Charmander, Squirtle, and Bulbasaur all at the same time, they tie him up to a tree.
A bit later, Ekans and Koffing have joined the rest of Ash's lost Pokémon for dinner. Ekans and Koffing have lost their masters as well. Bulbasaur repeats his hunch that their master's abandoned them, but Pikachu and the rest still disagree. Meowth begs for some food, but refuses to apologize, so doesn't get any. Suddenly, they all hear a loud rumble and see a huge Rhydon rear up over the trees. Pikachu unties Meowth, and they all run away.
Meanwhile, Ash and his friends are being chased by a Zapdos. Brock warns Ash that they need to find somewhere safe so that they can rest for the night. Ash mentally warns his lost Pokémon, and hopes that they are O.K.. At the same time, Team Rocket is being attacked by a Moltres. They run into a sign, and are knocked unconscious.
The next morning, Team Rocket wake up and run to the phone booth. Jessie calls their boss collect, but he hangs up when they recite their motto. James gets worried again, but Jessie has another idea. She knows that if they follow the telephone cable, they'll find civilization sooner or later. Suddenly, they see Pikachu coming over the hill. They get out to catch it, but they realize that it isn't the Pikachu that they know, it's a Pikachu that's over 50 feet tall! They dash out of the way, just as the huge Pikachu crushes the phone booth.
Meanwhile, Ash and his friends, as well as his Pokémon are having large problems themselves. Ash, Misty, and Brock are attacked by a huge Charizard, and the Pokémon are attacked by a large Blastoise when Squirtle tries to talk to it. They see a Venusaur, but Bulbasaur doesn't want to talk to it.
Team Rocket is now running from a huge Kabutops, and they reach a railroad cart. They climb inside and release the brake, only to discovered to be moving back towards the huge Kabutops. The cable that they were still holding, wraps around the large Pokémon's leg and Team Rocket ends up towing him behind them. They try to put the break on again, but the lever snaps off.
Ash, Misty, and Brock are still running, when they come upon the huge Pikachu. They then see Team Rocket in the runaway cart, towing the Kabutops. The cliff that they are standing on crumbles, and they fall into the cart as it passes by. The Pikachu is then also caught in the cord, and starts to be dragged along.
Misty points out in the distance and they all see Ash's and Team Rocket's Pokémon being chased by the large Charizard, Blastoise, and Venusaur. Ash tries to get the Pokémon into the car, but the brake is broken. They all go over a loop, and are now close enough to their Pokémon so that they can jump inside. They are all extremely relieved to have their Pokémon back. Unfortunately, the Venusaur, Blastoise, and Charizard get stuck in the tow of the cart, and start to be dragged along as well (which brings up the question as to how the cart can continue to move at such speed with all these large Pokémon being towed behind).
Suddenly, the cord snaps, and Ash and everyone in the cart are flung into the air. The cart then crashes into the Zapdos that was flying through the air, and it turns out to be a robot. The mechanical Zapdos takes a nose-dive into the other Pokémon and they turn out to be robots as well. The cart then carries it's passengers down into the water, and a boat passes by. This turns out to be a tour boat to the island, which happens to be a theme park type of place with mechanical Pokémon. The tour guide notices the broken Pokémon, and tells the crowd. Later, someone calls Team Rocket's boss and informs him of the news. Apparently, Pokémon Land was built by him.
Ash and his friends continue to walk along, and soon come upon the beautiful city of Porta Vista. Meanwhile, the Slowpoke is still fishing. He is about to get up when a Shellder latches itself to his tail, and he evolves into a Slowbro.