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Stormy Sea is the dungeon where you will fight the legendary Pokémon Kyogre. Obtainable by beating the game, you should see Medicham near your base. He'll say something about Lombre: go talk to him then to Whiscash who will give you dive and the location Stormy Sea.
Stormy Sea has 40 floors.
Unlike all the other legendary Pokémon dungeons, Stormy Sea will not have a rest area where you can save before battling the legendary so it makes that much harder.