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Shadow Pokémon's hearts are locked behind several 'Doors' in which the player must open to get to the Pokémon's heart. To open up a Door, the player must continue to battle with the Shadow Pokémon he/she would like to purify. After every battle, a small piece of the door you are working to open will turn white, indicating that you, and your Pokémon have became closer. You must open each door before you can actually purify the Pokémon.
How to Purify
Once you have opened up every Door to the Pokémon's heart you will need to travel to Agate Village and activate the Stone deep inside the Agate forest. Once you activate it, choose which Pokémon is ready to open up its heart and enjoy the scene afterwards. Your newly 'Pure' Pokémon will then gain experience points that it missed for being a Shadow Pokémon. The Pokémon will forget the Shadow Rush move. In XD, you can also purify by using the computer system in the Pokémon HQ.
Once you obtain the Flute you can purify one Pokémon from wherever you are. Once you use the Flute it will break.
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