Yeah if Raphaela killed Irene, wouldn't she be in the same boat as Priscilla who killed Teresa? Both attacks to Clare's mentor saviors were by order of the organization anyway. Irene also saved Clare from certain death and took care of her and even trained her giving her the quicksword attack that kept Clare alive through so much. Also tack on top of that that Raphaela sent Clare to Pieta. That could make any alliance really fuzzy.
Maybe half awakened claymores don't lose their consciousness completely when awakened ...
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