You have to go to the separate gyms. And then win each Gym battle
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in order for trader Pokemon to listen to you. you need gym badges if you have al 8 badges they will obey and if you have 3 or four badges is going to e hard to train Pokemon
You need all eight badges and you have to have beaten the Elite Four in order to capture Rayquaza.
8There are 8 badges, with the elite four after that.Hope this helpsPlease recommend me.
You have to catch one in emerald after the elite four in Pokemon emerald and you have to trade the other lati from Pokemon sapphire or ruby.
I think if you have all badges, and beat the elite four he should obey you. I'm sorry, but you'll have to be an excellent Pokemon hacker if you want Deoxys and Mew to obey you.