Only a few days after Twilight left the Mirror world in the movie "My Little Pony: Equestria Girls," things went crazy. At least a hundred new people poured into the town, killing everyone. Pretty soon, only about 50 people remained.
A couple months after Twilight left, she came back, apparently expecting to be able to visit her friends in the Mirror world. She did not expect to be held at gunpoint, only to see the man get shot and killed right in front of her, by none other than Rainbow Dash. She then learns that this has been going on for a while, and that the "Agency" plans to invade Equestria. She then goes with Rainbow Dash to look for Fluttershy and the mirror version of herself, while AppleJack goes through the portal to warn Princess Celestia.