Twilight and her five friends are transported during a botched spell, across dimensions to... Ponyville, Equestria? But not the same one that they knew. Sitting on a bench is Harpsy and Babar. The Doctoress avoids apples from an aspiring Applebuck. And in a library across town, six stallions join their forces as they try to decipher the appearance of filly look-alikes of themselves around Ponyville!

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.