It is a little north west of Lilly cove you will see a cave on water with a door everywhere
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You have to beat team aquas leader. His red orb will glow and kyogre will wake up.
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
you battle them