It's in a cave under water. It's near sootpolis.
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After you find the stolen submarine in Pokémon Emerald you must go to Mossdeep city. There you will obtain the HM Dive.
you have to use surf and go to sootopolis city from lilycove. then dive down and find the underwater cave.
Go to Route 128 and find some dark spots in the water. From there, use Dive. It should look like underwater canyons that stretch out for awhile. Explore around until you find a cave entrance. Once in, you should see a stolen submarine. Use dive there again to surface. Good luck
Get it back. People shouldn't steal.
You go in team aqua base beat everyone until you get to submarine. Beat the guy , go outside and they will be gone. Don't forget to find the master ball