Since the harmony crystals don't make a whole lot of sense,i like the idea of Twilight falling to to the dark side after her friends turn into dust,with her grief sucking out all her hope,she would slowly revert to how she at the start of the show and when pony racism starts again,she ends up feeling betrayed by the citizen she and her friends risked their lives for,so they can have a bright future.

Her answer to that would be making the unity crystals out of spite,forcing ponies to get along or else.