[@The One] The first Great War they weren't very much a part of, it was almost directly between Mewtwo's Army and the Legendary Council and their direct subordinates.

IF the Guild does end up existing, I'd say the most likely place would be the Shaymin Village, since it is her home. And she's got to have at least some members by this time.

Also looking over it again, the bit about Darkrai might be a bit much.