Twilight did pass her exam, but her magic did not flare up. Hatching a dragon egg was more of an optional test the parents could agree too. Because her magic never flared, Celestia’s attention was not caught by her. Twilight was left to enter the best academy in the land, but not as the personal student of Princess Celestia.
Only a few months later Twilight sees how alone she is in it, surrounded by unfriendly mares and stallions who were at least three years older than her, she begins to struggle in her studies. Shining is no longer there to help, and neither are her parents. She is convinced she is in this alone.
When one night a mare visits Twilights in her dreams. Nightmare Moon offers to teach her, and help her study, for one thing in return. Travel to the the abandoned castle of the two pony sisters by the thousandth sun celebration.