1.Put the Shadow Pokémon in your party and walk around with it.
2. Make it battle.
3. "CALL" the Pokémon during a battle when it's in "HYPER MODE" and make it "COME TO".
4. Leave it in the Daycare.
5. Use the "SCENT" item in the "COLOGNE CASE". By repeating the methods above the Pokémon will begin to become purified. The purifying process differs based on each Pokémon's nature.