It's been many days after Team A.C.T. went down to fight Groudon, and the people of Pokémon Square start to worry, so a town meeting is called. Blastoise, Octillery, and Golem agree to go down and save Team A.C.T. Here you might want to do optonal missions in places where high level Pokémon are because you're about to go down there as well. Level up to about Lvl 25 - to Lvl 30 because this is going to be a rough dungeon. Anyway, after a day or two, the rescue party comes back wiped out. After an inspiring speech your partner gives, rescue teams of all sorts gather their pride and march down into Magma Cavern.
Groudon cannot be recruited until after the end credits.
You will come upon Tyrannitar and Charizard on the second floor who say Alakazam is still fighting. You go down to Alakazam and with a flash of light he is gone but out comes Groudon, the continent Pokémon. Now comes a tough fight; just use the previous boss strategies and you should be able to pull out a win.
You return from Magma Cavern a hero, but don't relax yet. Xatu has seen a new peril, a falling meteor. The only way to stop it is to convince Rayquaza to help, and your team is up to the task.
To get here you will need the 'Teleport Gem' from Xatu. To get it, go to the dungeons list, click Sky Tower, and you'll meet Xatu at the peak of Great Canyon again. You'll use the Gem and be teleported to Sky Tower's 1st Floor. (Why can't they just teleport to the top?) You'll want to be levels 30-35.
This is the final chapter in your storyline. 25 large floors of monsters (some ghosts so watch the walls).
Note: To come back to this dungeon, you need the HM Fly from Wyvern Hill.