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Contrary to Ruby and Sapphire, you can only enter the Cave of Origin once during the game. Once Kyogre and Groudon have been awakened and clash in Sootopolis, you will be directed to the Cave. Within, you will find Wallace, who will talk to you about how to calm them. Mention the Sky Pillar to him, and then head there to awaken Rayquaza. Once the dragon awakens, it will Fly to Sootopolis, and calm Kyogre and Groudon. After that, you cannot enter the Cave of Origin again.

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11y ago

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