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You have to beat team aquas leader. His red orb will glow and kyogre will wake up.
you battle them
the master ball is in team aquas hideout. When u find the room with 4 pokeballs the one on the top left (I think) is the master ball.
surf to mount pyre then beat team aqua/magma then you can surf to team aquas hideout from lylicove after that the wailmers wil move and you can surf to modsep
In Emerald, go to Lilycove and jump down the ledges until you reach the stairs that lead down to the ocean. Go to the top right and Surf right and up until you see a cave. That is Team Aqua's hideout. (I only have Emerald, so apologies if this isn't correct in your game.)