You must defeat Team Aqua in their Lilycove City base (right next to the Wailmers). To gain entrance to the base, you must first go to Mt. Pyre and climb to the summit.
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You can't chase away them away, ya have to blow out the secret hideout and poof! Off they go!
u cant
first you have to battle maxie at the magma hideout (jagged pass) then go to slateport and watch aqua steal sub. Go to the aqua hideout (near the wailmers) and watch them run off with submarine. (dont forget to get master ball from hideout) now the wailmers are gone
If you have the hm surf, you can use it to get rid of the fog
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