Pokémon Mystery Dungeon: Blue Rescue Team and Red Rescue Team/Stormy Sea

To gain access to the Stormy Sea you must load the game after beating it and speak to Whiscash. Once you have gone through a cut scene learning about how to evolve Pokémon and switching leaders within dungeons, find Medicham near your rescue team base. Medicham will be laughing about Lombre and how he is unable to swim properly despite being a Water-type. Find Lombre in Pokémon Square to hear his version of the story, then finish up with another talk with Whiscash. Whiscash will give you the Dive HM and unlock both the Stormy Sea and the Solar Cave dungeons. In order to enter the Stormy Sea dungeon you must either have a Pokémon who knows the move Dive going with you into the dungeon or the HM itself in your inventory.

The Dungeon
This dungeon is challenging and is filled with water-type Pokémon. It has 40 floors and at the bottom is Kyogre. You should pack up on Max Elixirs, apples, HM dive and berries. You may bring a team as large as you want but in order to recruit the 4-star size Kyogre you can only have a 2-star size party when fighting it, so when you reach floor 39 say goodbye to enough party members to make room for Kyogre. For the first 10 floors, it is easy with weak Pokémon like Seel. After that it gets hard - the Pokémon are stronger, but there are more items to pick up. At around floor 25, the heat picks up as you face fully evolved Pokémon in large quantities. Make sure you know your types before the battles, an unlucky break of an Ice Ball attack could spell doom to a useful Grass-type teammate. On these more challenging extra dungeons that go beyond 30 floors, you should head straight for the stairs when you see them, or you will be bringing a toolbox full of apples along. Your party should be around level 35, so you may be able to tackle the Stormy Sea right after beating Sky Tower.

Items
Along with various orbs, there are different types of bands/scarves/ribbons(including Gold Ribbons). Different kinds of glasses can be found here as well(X-ray Specs, Insomniscope, etc.). Every kind of Gummi can be found here as well.

Boss Battle: Kyogre
Kyogre is on the 40F and will have a brief cut scene before fighting it. It is level 25 and has 540HP. It is extremely difficult to defeat Kyogre if you are around level 30 or below, as it can knock you out in one blow. Kyogre can be recruited on its first encounter and has a very high recruitment rate of 30%. Remember, the team leader has to give the final blow from an adjacent position in order to recruit. Kyogre has a size of 4 stars. The overall size of your team may not exceed 6 stars. With a bit of luck Kyogre will hand over the Seafloor Cave friend area and join your team.