they go in a deep sea trench in witch you need the hm dive. p.s. ITS TEAM AQUA.
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Team Aqua/Magma took it underwater. Dive a look around for a secret entrance underwater and go in it. You will see the submarine. Then one you are at the sub, go up to the surface above it and defeat team Aqua/Magma.
You go to their secret base just tright of lilycove
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.
you go to mount. chimney go down the side and a new cave will open up and it is a team magma hide out when you beat them go to saleport then when team aqua takes the submarine got back to team aqua hideout and beat them then they will go away also team aqua hideout is where you get a masterball
This may not be right but you got to go to Team Aquas hideout you will see a guy who is dressed as a part of team aqua saying jump wailmer jump you head up north to a cave which is where team Aquas hideout is. If you cant get past 2 Team Aqua goons you will have to go to slateport city where the submarine is.