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After you see the cutscene with Kyogre and Groudon fighting, you should be able to go into the Cave of Origin. Either Wallace or Juan (I don't remember which) is there. Tell him that Raquaza is in Sky Pillar. Go to Sky Pillar and go to the top. Click onRaquaza and go back to Sootopolis. After the cutscene, the gym should be open.

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