Puifying Entei, Suicune, and Raikou - Time Flute
Where each of the legendary Dogs are located there should be a item case where you can find a Time Flute or a person who will give you a Time Flute around that area. Instead of trying to get the Legendary dogs hearts open with battling you can easily use the a Time Flute on each of them which will Call Celebi and Celebi will purify them right then and there.
Note: The Time Flute is a one time use Item so you need three of them. One for each Legendary Dog.
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