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Go to Slateport City and there is an event that has Capt. Stern being interviewed. you talk to him and you'll read something about thank you for the sub or something. you go into the dock and you'll see the sub being stolen. after that happens go to Lilycove and where the Wailmers are, you have to surf up from there until you see what looks like a cave. you'll end up seeing the warp panels, like the gym in saffron city in Pokemon yellow, red, blue, firered, and leafgreen, you got to test the panels to find where they take you. in team aqua's HQ you also get the master ball, so be on the look out for it. its in a room with 4 poke balls on the floor. two of those are either voltorb or electrode. but once you find a room where the sub is you face one of the grunts and then the sub leaves. once you leave the cave the wailmers should be gone.

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