I've decided to put any idea's I may not get to here for others. If you see one you like, just go ahead and take it. Only two so far though, so deal with it.
 
Humans were ancient beings with immense power, however in a civil war most were whipped out, the few survivors were locked in time, but sometimes the locks break and one is freed. Anonymous is one who breaks out of his prison, and indifferent to the plight of ponies, but willing to hear them out and can be persuaded to help, such as slaying beast or recovering artifacts. After slaying perhaps a few problems the kingdom faces, a new one arises in the form of a black knight, a elite human committed to destruction and motivated by chaos. Yada yada, he becomes a villain with swathes of legions under him, and Anon and the Mane 6 must go full blown Paladin and save Equestria.
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Anonymous is a aged, hobo wizard (similar to: http://mattrhodes.deviantart.com/art/We-are-NOT-taking-the-wizard-256979744). He sits on giant spiders and eats out of zombie skulls and gives no fucks. Twilight is absolutely mesmerized in why he does these things, and wants to learn his magical secrets. The catch? He has no secrets, just spells. Twilight doesn't believe him when he says this though, and tries every method at her disposal to find out.