Luna is magically bound to her malicious double in a mirror world. Her evil doppelganger and Celestia the Desolate have all but dominated this other Eqiestria. Although Celestia is defeated, both Luna’s minds are magically broken to pieces. The only hope of getting everyone back to the world they belong is for Twilight, Rainbow, Fluttershy and the now silent Luna to find the princess's other self as she flees through the Chrystal Mountains.
I would imagine that both universes are finally seperated with both Luna being the last link. But I wonder what comes of Prime Equestria