Instructions
Fight and capture XD001, also known as Shadow Lugia. It is one of the more difficult Pokemon to catch due to its high defenses and special abilities. Use a Master Ball on Shadow Lugia, which is Pokeball capable of capturing any Pokemon instantly with a 100 percent success rate.
Go to the Pokemon HQ. This area contains the Purification Chamber, which is capable of purifying any shadow Pokemon in the game.
Fill each of the sets with Pokemon to achieve the "Best Circle" in each one. Do this by placing Pokemon in each set that are weaker than the element before. Example: water, to fire, to grass, to ground, to rock and back to fire. When you have filled all but the last set, you will achieve "Maximum Tempo" status.
Place Shadow Lugia in the last remaining set. A message will pop up saying, "Something is different about the Lugia! Maybe..." which is a signal that Shadow Lugia is ready to be purified.
Head over to the Pokemon Lab and enter the hologram chamber to see an image of Shadow Lugia. Press "A" to begin the purification process. When the action is finished, you have successfully purified Shadow Lugia in Pokemon XD.