A conversation with Discord causes Twilight to question the particulars of true harmony.

Discord’s lack of empathy and a pony's sensibility has been tolerated by Celestia, but while both the princesses and the bearers of the Elements of Harmony struggle with even more dire problems, Discord is forced into a lesson of his own.

Twilight might be required to take on the Spirit of Chaos - in all that that entails - to fully ensure that Discord's place remains with the friends he has made, and with her.

Interesting alternate or deleted scenes from my Sympathy Series

With the Doctor's help, Shining Armor finds Twilight again, only to find she doesn't know him.

Once there was a pony who could bring the dead back to life, who solved murders with a Griffon PI. Their investigations lead them to Ponyville & to team up with Pinkie Pie [Pushing Daisies crossover]