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You can catch Deoxys in Pokemon Emerald version at a Place called Birth Island.
You have to have a Birth island pass card to go there first of all you can get that with cheats but to get it you have to talk to an old man in moss deep city and he will give you the pass but you also have to talk to a sailor in slate port city and he will Tell you a story about an island in his past and he will say he saw a Pokemon strange as his eyes could see attacked him as he tried to catch it in a game he thought was tag then he will say you look like a Pokemon trainer yourself would you like to go for a ride to the island for you self you answer yes on no and if yes he will take you there.
Deoxys will be a little triangle sitting on the island the triangle will move and you have to find it five times the it will transform into Deoxys after he gets tired of you getting him and he will attack you and you will go into battle.
When i caught him i didn't have a master ball but i had 30 ultra balls. he Will battle you at level 30 and you should bring a psychic type or an electric type with you that has the move of hypnosis or stun spore and use it on him and he will be more easy to catch but try not to bring legendary Pokemon with you or any strong Pokemon above level 45 or he will be easy to defeat and he will flee.
P.S. if you have a rare or even shiny Pokemon in your party deoxys will be shiny when you fight him.
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