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!
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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.
To find your Secret Base, talk to the short guy in a house in western Mosdeep City. He will mention a base on a certain route. Go there, and find your Secret Base on that same route!
go to mahogony town and find their secret base in the house with the old lady and beat them there with the champion from the Pokemon league lance
Get the TM secret power teach it to a Pokemon then find either a tree with vines, an indent in the wall or a big bush use secret power on these to create your own secret base.
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.