Heres an idea, The Daleks invade Equestria after the Master opens a portel allowing the Daleks to cross over from our universe to the equine universe, the Daleks capture many of the citizens of Equestria and exterminate them and mutate their corpses into Daleks (A bit like what the Dalek Emporer did in "The Parting of Ways"), the Doctor, Twilight and the Master (Who was betreyed by the Daleks) were chained up together to be exterminated, when the Supreme Dalek asks the Dalek Emporer if they should kill them now, the Emporers casing opens up to reveal Fluttershy inside, the real Emporer was killed by the equine UNIT (United Neightions Intelligance Taskforce) and Fluttershy used the empty casing to save her friends and opened the doors into the Dalek Flagship allowing UNIT to bust in and wipe out the daleks