The heroes come to the A-B-C Islands, where they meet up with Professor Birch. The Professor wants to study more about Clamperl's evolutions, Huntail and Gorebyss. They also accompany two children, who are angry at each other, for they want to evolve Clamperl that goes against their principles. Birch, however, finds something that can settle the trouble, and give Team Rocket a new opportunity at stealing Pokémon.

Due to a twist of fate, the heroes get captured by Team Magma and face their leader, Maxie. After Maxie explained his goals, Team Aqua's Shelly frees Kyogre and reports to her leader. In a moment of confusion, Pikachu takes the Blue Orb, which gets absorbed into him. Just as the heroes try to escape, Ash gets captured, while Team Aqua's leader starts controlling Kyogre. However, an unexpected help arrives, a man whom Ash and Brock have met before.