In the future, Where Equestria had been left to ruin, The Main 6 had been disbanded. They were left to do things that weren't exactly done for harmony.
Twilight is now an outlaw living in the woods, Experimenting on poor souls that got lost in them. Applejack, associated with her family & Flam, try to take revenge for Flim. Twilight's experiment finally paid off, But it would be the death of her