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Silver Trench
After rescuing Latias from Pitfall Valley, aim to recruit Articuno, Moltres, and Zapdos from their respective dungeons. (Frosty Forest, Mt. Blaze, and Mt. Thunder.) After doing both, visit either of the three in the Legendary Island Friend Area to obtain the Vortex Stone from Articuno. It will give you access to the Silver Trench, to find the guardian of the sea.
Inside the Dungeon
This is another 99 floor dungeon, and you need Dive to enter. Max Elixirs stop appearing at B20F, and Blue Gummis and Grimy Food stop at B30F. Bring extra food and elixirs, because of a large number of Grimy and PP-Zero Traps in the dungeon. Fixed monster houses appear on B15F, B35F, B55F and B75F, on the first room of the floor.
Wild Pokémon
Lugia
On floor 99, you will find the guardian of the sea, Lugia.
Lugia has a 99.9% recruitment rate, so be sure to have your team size down to two stars when you battle it.
Meteor Cave
After recruiting Lugia, Xatu will appear outside your team base. Soon after, Blastoise will come by, and talk about seeing "weird things" in a dungeon. Xatu names it Meteor Cave, because it was made from a chunk of the destroyed meteor. Xatu then gives you access to the cave.
Inside the Dungeon
This is a unique dungeon. Only one Pokémon can enter, and only three items can be brought, four if you bring a held item. The only Pokémon you will find is Deoxys. There is one on each floor, and you have to defeat it to unlock the stairs. It will be in either Attack, Speed, or Defense form. This continues for 20 floors, until the end. It is very useful to bring Iron Thorns/Silver Spikes/Sticks to the dungeon, throwing them will be able to defeat each Deoxys easily.
Pokémon
Deoxys (Normal Form)
On floor 20, Deoxys is found in its recruitable Normal Form.