To get past the Wailmer you wil have to defeat team Magma/Aqua. The base is to the north of the Lilycove city beach (Don't forget ot get the masterball when your in the base). One Archie or Maxie is defeat and he flees, you are free to go east to Mossdeep city.
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You use a super rod in lilycove city.
In Dewford Town, you can use your super rod to catch a level 20 - 45 Wailmer. In Lilycove City, you can use your super rod to catch a level 25 - 45 Wailmer.
You have to go through the hideout which is the cave slightly north of the wailmer. In the hideout you have to beat the admin at the end and see the submarine sail away, you can also get a masterball in there too
you need to have 6 badges and surf when you get there team aqua will be there and you cant go any further because wailmer are blocking your way hope this helped
You'll have to go into the cave that is just north of them and defeat team Magma/Aqua. Then you might have to fight Groudon/Kyogre. After that they should have moved.