Following the Tirek incident, Equestria is once more at peace and festivities abound by ponies grateful for their freedom. Princess Twilight Sparkle and her friends have perhaps the greatest deal to celebrate, especially with the key-bearers who helped them to access Rainbow Power.

So Twilight decides to spend quality time with Discord—lord of chaos and final key-giver—investigating the Tree of Harmony, and the two friends must learn to work together towards a common goal while coming to trust each other. But friendship is not always easy, and when a struggling Discord receives a visit from a shadow that claims to be Tirek and threatens to destroy the mane six out of revenge, it tests their newly forged bonds and reveals many ancient secrets along the way.