Once you have beaten team aqua and Archie has ecscaped, then you have to surf to mossdeep city, and from there try to find the deep sea trench. When you find that, there will be a cave that you have to explore. When you find kyorge, Archie will wake it up and all this crazy stuff will happen.
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You have to beat team aquas leader. His red orb will glow and kyogre will wake up.
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They are in their bases. magmas is on the way down mt.chimney. And aquas is in the cave near lilycove city. To open up magmas base you have to go to the top of mt.pyre where you will have to battle team aquas goons .Once they have gone talk to the old man if he doesn't give you a magma embelem talk to the old lady Once you have that go down mt.chimney and the screen will shake and it will say somthing. you should see a cave if you go into it this is magmas base. once you complete that go to lilycove city and surf to aquas base.
go to Lillycove city and then go right to the beach and surf up and then you go into the cave entrance and its really the entrance to team aquas hideout!
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