3 years ago, Princess Celestia ascended to The Great Beyond, leaving King Flash Sentry and Queen Twilight Sparkle in charge of Equestria. Twilight has the Tree of Harmony uprooted from the Everfree Forest and re-planted in a garden in Canterlot, but Twilight doesn't realize the consequences until Equestria is once again threatened by the black vines from the Everfree Forest.

After exterminating the pesky weeds, Twilight becomes unpopular with her subjects, and her family is put in danger.