you have to use surf and go to sootopolis city from lilycove. then dive down and find the underwater cave.
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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.
Get it back. People shouldn't steal.
It's in a cave under water. It's near sootpolis.
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.
Dive near route 127 near Mosdeep city then go inside the cave where the submarine of Capt. Stern then dive back up