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Go to the Seafloor Cavern slightly South-East of Sootopolis and defeat the Team Aqua/Magma grunts. You'll need a Pokemon with Rock Smash and a Pokemon with Strength to get through. You'll reach 2 fairly easy puzzles of boulders that need to be moved with Strength. Defeat another member of Team Aqua/Magma in between these puzzles. After this, you'll need to defeat Archie/Maxie and you'll discover either Kyogre (if you're playing on Sapphire) or Groudon (if you're playing on Ruby). This will cause either a massive rainfall (Sapphire) or severe sunlight (Ruby), and you then go back to Sootopolis and up to the entrance to the Cave of Origin. The gym leader of Sootopolis, Wallace, will explain what to do after that.

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Q: What do you do after you find sootopolis?
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