In Slateport City, Captain Stern reveals that if Team Aqua and Team Magma have reached the Seafloor Cavern, then it'll be impossible to reach them. He then calls Gabby and Ty to his side and reveals that even though he doesn't know what the two teams are after, he knows that there is an enormous power at the cavern.
At the Seafloor Cavern, Amber and his Pelipper attack the slumbering Kyogre, which allows it to awaken. Kyogre dives down into the ocean, and Archie gloats over his victory over the face that they awakened their Legendary Pokémon faster than Team Magma did. Due to Team Aqua having awoken their Pokémon first, Kyogre will have the advantage despite the two being evenly matched.
In Fortree City, the Gym Leaders look in horror at the flooding happening all over Hoenn. The destruction pressures Winona into increasing the emergency. They are soon called by the Pokémon Association Chairman, who reveals that a massive entity is swimming through the water, and the tsunamis are caused by it surfacing. The Chairman instructs Winona to alert all of Hoenn about the situation.
Suddenly, Kyogre emerges from the water, leading to the Chairman telling Winona to inform the townsfolk. As Kyogre swims through the water, the Pokémon Association informs Hoenn of Kyogre's awakening. Kyogre approaches the Abandoned Ship, which it easily blows apart with an attack. The attack sends Plusle and Minun flying, and they are carried away by the waves produced by Kyogre. Suddenly, Kyogre breathes a substance into the air, which causes a powerful storm to start.
Back at the Seafloor Cavern, Tabitha repeatedly attacks Groudon with his Torkoal. Eventually, he awakens Groudon, which immediately dives into the ground in order to surface later. Maxie assumes that Archie thinks that Team Aqua has the advantage due to their raising the sea level and awakening Kyogre first. However, Maxie has Tabitha present him the Red and Blue Orbs that Blaise had obtained at Mt. Pyre. Maxie activates the orbs and uses them to control both Legendary Pokémon to give Team Magma the advantage.
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