Continuing their adventures in the Orange Islands, Ash and his friends have stopped off at Mandarin Island. After recalling Lapras, the trio hear a commotion, and notice a Grimer, Voltorb and four Magnemite attacking their Trainers. Eager to investigate, Ash and the others run to help. However, as Pikachu approaches, it stops. When Ash inquires as to what is wrong, Pikachu just glares at its master. Out of nowhere, Togepi jumps out of Misty's arms and glares at its Trainer as well. Pikachu and Togepi then join the other Pokémon, while Voltorb explodes, distracting Ash from rescuing his Pokémon. When the dust clears, Officer Jenny has arrived, but the Pokémon are gone.
At police headquarters, Jenny explains that for some time, Pokémon have all been disobeying their masters. The only Pokémon that doesn't appear to be affected by it is a Gastly. Jenny explains that she is hoping by using Gastly, they will be able to figure out what is going on. Ash and the others vow to help as well.
Meanwhile, Team Rocket has arrived on the island. While Jessie and James want to go exploring, Meowth becomes angry with them, saying they have important business to do. Suddenly, Meowth pauses. When Jessie and James ask him what is wrong, he takes off. Team Rocket follows Meowth, and end up in a large room. As they get up, they notice Butch and Cassidy looking at them. After both sides say their motto, Butch and Cassidy explain that they are stealing all the Pokémon on Mandarin Island for the Boss. They present proof by showing all the Pokémon they have stolen so far, which includes Pikachu, Togepi and Meowth. Impressed, Jessie and James decide to steal the Pokémon Butch and Cassidy have taken.
Jessie sends out Arbok and Lickitung, while James sends out Weezing and Victreebel. While Victreebel bites on his head, Butch snaps his fingers. A Drowzee hooked up to a machine appears. As Jessie and James question about it, the Psychic-type begins using Hypnosis, causing all four of the Rocket's Pokémon to turn against them. Butch and Cassidy explain that they have Drowzee hooked up to an antenna which strengthens and broadcasts it's hypnotic power all across Mandarin Island, which has allowed them to take control of all the Pokémon on the island. Having revealed their plan, they decide to get rid of Jessie and James and set their own Pokémon (including Meowth) onto them.
Jessie and James are later found unconscious and taken to the Pokémon Center. When they awaken, they are with Officer Jenny, Ash and the others. After explaining that they witnessed Butch and Cassidy with all the stolen Pokémon, Ash tries to convince them to infiltrate their base again. The duo refuse, until Jenny convinces them that if they do this, they will be thought of as heroes. Liking this idea, Jessie and James agree to help out.
Looking through a surveillance camera, Butch and Cassidy see Jessie and James roll a large cart up to the entrance of their headquarters. It is filled with Poké Balls. Jessie and James tell the other Rockets that they would like to make peace, and have brought hundreds of Pokémon for them. Butch and Cassidy are skeptical, but let the duo in anyway. As they enter, Ash, Misty and Tracey jump out and demand Butch and Cassidy return the Pokémon. They refuse, saying that with the help of Drowzee, the Pokémon on Mandarin Island will do whatever they want them to do. Using Drowzee, they have all the Pokémon attack the Trainers. All the electric, fire and water types combine their attacks into a super-powered blast however Gastly protects them from it.
Suddenly, Ash gets an idea. After Pikachu shocks him, he gets up, taunting Pikachu into launching another attack. This angers Pikachu, who tries again. Ash keeps dodging the attacks, all while taunting Pikachu. Everybody is confused as to what Ash is doing. As Gastly starts to weaken, Ash gets in front of the machine controlling Drowzee and taunts Pikachu into giving it everything it's got. Pikachu launches a massive ThunderShock, which strikes not only Ash, but the machine as well. As a result, it overloads and explodes, causing Drowzee to lose control of all the Pokémon.
Misty happily runs up to Togepi, who, upon seeing her, jumps into her arms. Ash, injured and tired, looks up to see Pikachu jump into his arms. The other Pokémon are released back onto the island, and run off to find their Trainers. However, Butch and Cassidy refuse to let Ash and the others leave. They challenge them to a battle, and Ash accepts. Using Drowzee, Butch and Cassidy are able to confuse Pikachu. Then, they have the Psychic-type use Metronome. Tracey comments this is trouble, as they don't know what move it will use. At the same time, nobody notices Togepi using Metronome as well. When it completes the move, an explosion sends Butch, Cassidy and Drowzee flying, and their headquarters destroyed.
After the duo is arrested, everyone wonders where the explosion came from. Many attribute it to Drowzee's Metronome having backfired on itself. Ash and friends then bid Mandarin Island farewell and head off on their next adventure.