Long ago, the ruler of the dragon race, Bahamut made peace with Celestia when she founded Canterlot. Dragons and Ponies lived in peace for the first time. Bahamut had left one day after feeling a great evil arising in the distance. He had disappeared for many years until one day he returned. Filled with an uncontrollable rage, he attacked Canterlot. Celestia had no choice but to seal him in stone until he could be cured. After the elements of harmony transferred to Twilight and her friends and Luna lost control of her portion of the elements, the spell weakened. On a still quiet night, Bahamut broke free. He destroyed all of Canterlot and melded the Castle into the mountain creating a labyrinth where he hides and frees all the other sealed evils Celestia and Luna had stored away in the depths of the castle.
Years later, Aura, a unicorn that Twilight had found in the wrecked remains of Canterlot, rallies with his friends to traverse the dark labyrinth in hopes of finding a way to end this nightmare.