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Sky Pillar will not open until it becomes essential to the storyline. Once this occurs, Wallace will meet you at Sky Pillar and grant you entry in order to awaken Rayquaza. After completing this event, Sky Pillar will remain open.
From the second visit onwards, the Mach Bike is required to navigate to the top floor.
Just go there after you get through Groudon and Kyogre's battle.
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