This is pretty complicated.
The submarine works like a maze. There are a few options every time you go into the next platform. It's not random, but long and complicated.
The only thing you can do is just trying all the passages randomly until you succeed.
It may take only a few several minutes. It is easy. Don't give up if you don't success. Just try and check any possible passage there. Eventaully, you will be able to finish this and find the stolen submarine.
Additionaly, you can find there a MASTER BALL!
Look for it good.
After you find the stolen submarine in Pokémon Emerald you must go to Mossdeep city. There you will obtain the HM Dive.
It is almost exactly in between Sootopolis City and Ever Grande City on your map. Go there and dive underwater. Search around underwater and eventually you should find an underwater cave containing the submarine. When you find the submarine, head to the surface.
it is in team aqua's base (the one where they had the submarine)
you first go to steven to get dive and dive dvie
Go back to Slateport town. Inside the ferry building, you will find captain stern and the submarine being robbed by Team Aqua.
in your moms belly
The submarine belongs to that scientist guy, you're not allowed on, you have to learn dive then find the place they are exploring, but there is a scale model of the sub in the museum.
It's in a cave under water. It's near sootpolis.
Lieutenant Pimple and the Stolen Submarine - 1914 is rated/received certificates of: UK:U
Catch the submarine Pokémon and beat the crap out of the Elite Four.
go get a life
you will find team aqua in the under water cavern near the dive point in sootopolis