At the final alternate timeline in the season final we see Twilight, Spike, and Starlight in a desolate Equestria void of life. But what did this? In all the timelines a villain the elements faced had made havoc on the land. Sombra, Chrysalis, Nightmare Moon, Discord, Tirek, The Flimflam brothers. All did something; but what did this? Someone or something must have destroyed Equestria and on a level to Genocide and destroy as far as we know all life. Is it some villain we've never seen before? Or is it someone we know. Someone who only had the chance to do all that destruction in that timeline. We may never know but if it is on the shoulders of some living being then what we do know...is that in the current timeline. They're still out there.

But hey that's just a theory. A FIM theory

4996269 gl
Given the fact that we never seen the cutie map controller would have somthing do this with the unknow villian in the End timeline.

4996269
It was Twilight Sparkle.

4996621

Tyrant twilight

4996398

Hmm. Still in the dark