So, game Yvonne obtained a dark power to combat Elsa's overwhelming magical prowess, and there is a dark-cloaked Yvonne inside Evie trying to make her hurt Elsa.
Elsa has a future(?) version of her that seems to have traveled back in time to help keep Evie off the evil path.
If this is supposedly the second run through of the story, it could be that the dark power from the first run has also traveled back in time, and manifested itself as the Villainess System in order to force Evie to become evil again and ensure its continued existence.