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.

The heroes arrive to Mossdeep City, but learn the Gym Leader Ash wants to battle is at the Mossdeep Research Center. Once they arrive there, the heroes met up with Tate and Liza, who just had a battle. Learning these two are duo of Gym Leaders, Ash is surprised he has to fight them in a Double Battle. While spending some more time at the space center, Max and Tate go to a space shuttle, only to encounter Team Rocket, who wants to steal the space shuttle.