With Earth now combined with Equestria, everyone is switching between being humans, and being ponies. When Twilight tries to get Ponyville under control, she discovers that Equestria has a Doctor of it's own, and that he's one of the few people who can help. Once the real Doctor escapes the clutches of Omega, he returns to Canterlot High to discover what has happened to the world. With the help of his copy, The Doctor must stop Omega, before Earth collapses on itself.