go to the slateport city harbor outside and you'll see capt. stern interviewed. when you go inside the harbor you'll see team aqua escaping with a submarine. go to lilycove city then to the aqua hideout. then beat every grunt on your way. when you beat the last grunt in the hideout, he'll tell you the boss has escaped. go outside the hideout and the black things will be out of the way on the water, letting you through.
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When you enter mt pyre you can go up the stairs to get items, but team aqua is actually through the other door on the 1st floor. Then you just follow the path up.
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 get if from your Rival, after defeating team Aqua in the weather institution, who gives you Castform, but you must beat your rival before receiving the hm.
Go to Mt. Pyre. Stop Team Aqua. A woman will give you the Magma Emblem. Go to the Jagged Pass. The floor will rumble and a door will open. Go there. That's Team Magma's hideout. Battle Maxie. Then go to Slateport. Team Aqua will steal the submarine. Then you can finally go to Team Aqua's hideout. (A master ball is there) And fight the executive. Then the Wailmers are finally gone.
after getting into team magmas hideout