Applejack awakens to find herself in a new world, in a body not her own. Her Earth Pony magic is intensified to dangerous degrees, and she's surrounded by threats of a like she's never imagined. She'll have to fight to return home... if she even can.
After the defeat of Tirek, a special letter arrives with news from a secluded town in the middle of Nowhere. Now the main six are tasked with finding out what happened there, and who this Mister Baker really is.
A human soul is stuffed into King Sombra's body. Having no idea what's going on, and thinking he is in some kind of coma, he just casually strolls into the Crystal Empire.