Hi! I've been longing to recruit Rayquaza... How could I do it?
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In order to recruit any Pokemon, be it common or legendary, you should try to be a high level. The higher your level, the easier it is. Also, some common Pokemon can ONLY be recruited by certain level Pokemon. Nevertheless, you still need quite a bit of luck. Just keep facing it. It will eventually offer to join your team. Friend Ribbon also helps.
If you have already destroyed the meteor (if you haven't then just keep playing the game till you do) than later on when you have opened up Wyvern Hill you have to go to 30F (with a key I think) to get the Fly HM. This will allow you to return to Sky Tower, and you can recruit Rayquaza. P.S. You can get keys at Solar Cave (throughtout the dungeon, but rarely), Desert Region (19F and 20F rarely), and Western Cave (throughout the dungeon).
If you are still looking for help with this game we have more questions and answers for you to check.