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You go to Mossdeep and defeat the Gym leaders there. Then Steven will give you the HM move dive. Then you can go south of Mossdeep to find a trench. You use dive here (with a pokemon that learned it), and go south until you find a cave area . Go in and there should be the submarine. Press B (this reverses dive) and you should come up to where the team took the submarine. Go into the cave located here and you should find Team Aqua. At the end of the cave you will find Aqua Leader Maxie trying to awaken Kyogre. Just like with Groudon, Kyogre just leaves.
Then you may go to Sootopolis and see the show.
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Where do you find the submarine that team aqua stole?
in the back of the base, but they get away with it.
What do you do after team aqua stole the submarine on Pokemon emerald?
Get it back. People shouldn't steal.
Where does Team Aqua steal the submarine?
At a cave under water in route 128 :)
Where do you find team aqua after they steal the submarine in Pokemon Sapphire version?
you will find team aqua in the under water cavern near the dive point in sootopolis
Where is capt sterns submarine in emerald?
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.
