Before the Princesses, Discord ruled unopposed over all of Equestria. Most of the time that is, when a certain time traveler isn't interfering in in his own infuriating way.

The Doctor, the last surving Timelord of Gallopfrey, travels through time and space, along with his companions from Equestria.

The Missing Cutie Marks: The Doctor is in, making his debut in Equestria! He soon finds that not all is well, however, when ponies’ cutie marks mysteriously go missing… The "disease" is spreading, and the Doctor must find out what's causing it with the help of his new friend, Twilight Sparkle.