Going back in time, The Doctor takes his companions to the early years of Princess Luna, and Celestia.
On the way, they see the defeat of Discord, The destruction of the Crystal Kingdom, and the eventual transformation of Luna, into Nightmare Moon. All the while, they're searching for the answers to the Elements of Chaos, and the role that they played in these events.
And in the end, everypony will see the Princesses in a new light.
Offshoot of: Off The Record
http://www.fimfiction.net/story/22486/my-little-pony-friendship-is-magic-off-the-record