Black Aether came from Mystic Rune, but not many know where Mystic Rune came from and despite the connection he has to the royal family, he was wiped from history. The only ones who remember are the Princesses.

"Know that there was once many alicorns and that among them a Dark Alicorn arose, and brought equestria to it's knees, and that he was cast from that role and stripped of his power. He needed that to happen, for it was then he found true power."