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.)
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you battle them
You have to beat team aquas leader. His red orb will glow and kyogre will wake up.
look up walkthroughs on youtube
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!
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.