Using Twilight’s friendship journal Sunny found her in depths of a remote cave, guarding what was left of her dear friends, now long gone. She was there for hundreds, maybe thousands of years, alone and deep into an immortal sorrow.
I always enjoyed the theory that Twilight sustained wounds during her bash with Tirek, and losing her magic right after briefly robbed her of near-invincibility, so she has some scars even afterward. Seeing a few more scars here kind of alludes to that same thing, that losing her magic made her vulnerable over the years.
Ok that is one of the most depressing things I have read today. It´s remarkable that Twilight is even sane at this point after so many years. I fell really sorry for my dear lavendel pone. I might not like the idea of Twilight ever loosing her friends (thats why I find ways around it), but this idea is certainly a good one.