Once upon a time,

Aura Guardians were the protectors of the land.  No one knew where they came from, or understood their powers.  Some said that they slew Pokemon that attacked villages.  Others said that they saved Legendary Pokemon.  Yet others thought that they disguised themselves, to help the weak, the poor.

However, a trusted Aura Guardian turned.  This man and his Greninja could fuse in a special way.  Unfortunately, the pair became power hungry.  They ordered villages to pay tribute.  Other villages began to fear Guardians.  Burning them at the stake, lest they turn also, and burn their towns.