It has been 10 years since the Princesses and the Bearers of the Elements of Harmony disappeared, and 7 years since the beginning of the Discordian Civil War. Unicorns, under Discord's control, fight for dominance, while Equestria fights to stay alive.
Now, hope has returned. The Bearers are back, and they're ready to end this war, once and for all. All they need to do is venture outside of Equestria to reclaim the lost Elements, battle the unicorn nation of Utopia for the Element of Magic, and find and defeat Discord. Easy, right?

One Last Mission diverges from cannon during the events of Season 3, shortly before Twilight Sparkle would have ascended. She and the others vanished three years after the return of Princess Luna. This story begins ten years after that.