Ten years have passed since the sorrowful day when the Bearers of the Elements of Harmony disappeared. The last seven have passed in civil warfare. Discord controls the minds of almost every unicorn in Equestria, and they have formed their own nation: Utopia. Equestria fights to survive, but it's a losing struggle. The Elements of Laughter and Generosity possessed by Equestria can barely stand against the near constant onslaughts by the Element of Magic, and cities are being destroyed as often as they are taken. The Elements of Loyalty, Honesty and Kindness are lost beyond the borders of Equestria. All seems hopeless.
Then, the Bearers return.

Set ten years after the events of Season 2, from which point the story diverges.