I think it's around Route 127... Down from mossdeep city....
You will find the long underwater way...Drive there.... Just go down then you will find the cave .... Go in and....... SHADAA! Submarine!!
you dive near sooptopolis city and go in a cave and it is there and you surface and battle them all and it starts raining heavily.
James
Team aquas base where they first hide the submarine. It's in one of the rooms
127
in team aquas hide out
lilycove city or something like that
near team aquas hideout in sapphire. but in emerald it is on MT. chimeny
Keep progressing in the game and you will find it. East of Lilycove city.
you don't its never seen again
in ruby/sapphire they are in petralburg woods, rustobo city, near the lilicone city and near the sotopolis city.
you go to the team aquas submarine then use dive then your in sea floor cavern and make sure you battle everyone
it is in team aqua's base (the one where they had the submarine)
Team aqua does not own a hideout in ruby, only magma does, however in sapphire it is vice versa, no magma, just aqua.
beat all 8 gyms or in sapphire emerald or ruby you go to team aquas base or you could game shark it