Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

"Millennium Wake: Part II" can be found here!

Rarity awakes after a thousand years of forced magical slumber. How will she cope with a world where everypony she ever knew and loved is long gone, a world that has moved on without her?

Editor in Chief: GaruuSpike

Now has a TV Tropes Page!
http://tvtropes.org/pmwiki/pmwiki.php/Fanfic/MillenniumWake

Additional Editors:
Darthrex
Zervziel
SennenRyu

Cover art by:
ShadowSolstice
at
http://browse.deviantart.com/?q=millennium+wake#/d59hfdd