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.
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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
Pokemon Emerald, Ruby, and Saphire.
You need to get past the Team Aqua grunts at Lilycove Town to advance on Pokemon Emerald. In order to do this, you first have to beat Team Aqua grunts at Lilycove Town.
at there hide out
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.