An imaginary friend. That is what Fluttershy and Rainbow Dash had decided the mad pony in the box was, but the raggedy doctor was far more than that. When the supposed-imaginary Doctor appears in present day Ponyville, looking as though mere seconds has passed since they last saw him, Rainbow Dash and Fluttershy are in for some very real trouble.
((Heavily inspired by the Doctor Who episode "The Eleventh Hour," as such it will contain plenty of references but the story goes in its own direction. Conceived as an 'episode' with subsequent sequels acting as other episodes in a larger series.) )