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I think they weren't evil, and that the AI isn't entirely reliable. Remember in the Scarlet/Violet book how it's mentioned that Heath blacked out and wrote one of the pages without remembering having written it?
I think something similar must've happened to the professors while they were down there. Maybe the third legendary or the crystals influenced them somehow to do what they did, maybe twisting their dreams in order to make them do what they ended up doing.
