I love Doctor Who, and i love FiM. I know this has been done so much, but maybe I can give you all something you'll like.
A grief-stricken 10th Doctor deals with his own mortality, but before he can continue with his own canon storyline, a PLOT DEVICE transports him to Ponyvile, and his body adapts via glorious regeneration! Time for wibbly-wobbly, timey-wimey!