Sapphire and Ruby dive down on Sapphire's Relly to the Seafloor Cavern. On the surface, Wallace wishes the two luck on their mission. Wallace decides to help Brawly and Roxanne in order to reduce the destruction while Ruby and Sapphire go to retrieve the Red and Blue Orbs. Despite wanting to help fight, Winona decides to stay at the command tower because of her orders from the Pokémon Association.
Winona decides to call the Pokémon Association Chairman, but is unable to get a signal due to the weather. Wallace quickly notices a giant figure approaching them that is obscured by the heavy rain. The figure is revealed to be the Pokémon Association headquarters, which is being suspended in the air by a giant balloon. The Chairman reveals that because of the fires spreading in Lilycove City, he had to turn the headquarters into an airship in order to get to safety.
The Chairman tells Winona that he is taking over her duties, allowing her to go out and fight with the other Gym Leaders. Having heard her orders, Winona prepares to go and help Flannery and Wattson battle Kyogre. The old couple ask the Chairman if he can help search for Tate and Liza. The Chairman agrees to this, but states that it won't be an easy task.
Wallace and Winona briefly shake hands before seeing each other off. Suddenly, a man flying around in a small UFO approaches the headquarters airship and sneaks inside. Somewhere else, Professor Birch listens to a call asking the people of Hoenn to seek shelter. He notes that because of the raging floods and heat waves, going outside would be considered suicidal. Even though he notes that it's dangerous, Birch remains outside while atop of a tree.
Birch apologizes to Treecko, who was going to meet its Trainer today, but cannot due to the flood. Birch impatiently waits for the Trainer, who had said they would arrive no matter what, due to the flood potentially hitting soon. Suddenly, a wave of water crashes into the tree Birch is holding onto, sending him into the water. The waves knock the bag with Treecko and the third Pokédex out of Birch's hands and carries them away.
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