Princess Peach Toadstool of the Mushroom Kingdom has come to Equestria on important diplomatic business, bringing with her the superstars of the Mushroom Kingdom, Mario and Luigi. But, when Discord is released, and aids Bowser's forces in invading Equestria and kidnapping Peach, Celestia, and Luna, Twilight and her friends must work together with Mario and Luigi on an adventure spanning two kingdoms, to rescue the princesses, defeat Bowser and Discord, and return Equestria and the Mushroom Kingdom to their former glory.

When one of Fluttershy's dear animal companions wanders into the Everfree, she sets out to bring him home safely - but what she finds at the center of the forest is something she didn't expect, and something that ushers in a change to her world that makes each day darker than the last.