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I beat Rayquaza last year, and I went to that underwater cave, but I got killed o the 40th floor. Can anyone tell me a bit more about the cave?, like what Pokemon are there, and how many floors?

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There are in fact 2 Dungeons after Rayquasa that have an water theme, Stormy Sea and Silver Trench. Both present powerful Water and Rock type enemies.

Stormy Sea is fairly difficult, sporting 40 floors and 20-35 Lv Pokemons and a powerful final boss.

Silver Trench on the other hand is undoubtedly one of the biggest challenges in the entire game, containing Lv 18-45 opponents spread across 99 floors and one of the most destructive bosses in the entire game.

If you want to venture into these dungeons, bring powerful Electric, Grass and Fighting types to deal with the monsters of the depths.

http://bulbapedia.bulbagarden.net/wiki/Silver_Trench
http://bulbapedia.bulbagarden.net/wiki/Stormy_Sea

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Is the final boss Kyogre?
In Stormy Sea, Kyogre is the boss, and in Silver Trench Lugia is the final boss.
... ... ... because if it is, then I am screwed. I'm playing as a Feraligatr and Charmeleon, and the only other pokemon that I have that are decent are 2 Duskulls and the Absol.
I was planning on getting an ampharos anyway. Are they in Mt. Thunder?
Feralgitar is an excellent Pokemon to bring, maybe learn it Brick Break though. And, if you can, visit Lightning Field, there are tons of powerful Electric types there.
Where is lightning fields?
It is another dungeon, full of Electric types. Recruit one or two, and you should have an a lot easier time getting through. You need to have found HM Surf in Solar Cave to get to the Field.
Ok, Thanks!