This story is a sequel to Javelin
A war against the dragons that was prophesied to occur centuries in the future has just reached its devastating conclusion.
Twilight Sparkle finds herself in the blasted ruins of Equestria, trying to remember what went wrong, and desperately hoping that she is not the last pony left in the world.
Two days earlier, Vinyl Scratch wanders the streets of Canterlot as an agent of Celestia, witness to a world turned mad by war and falling prey to riots and conspiracies.
A prophesy once stated that Vinyl Scratch would save Celestia and all of Equestria...but the power of prophesies has been broken forever.
This is the conclusion of the Betwixt Silver and Gold series, which began with "Javelin" and most-recently included "Whopper of the Year".
The story is Alternate Universe-tagged because the idea for it originated before Season 2 began. Well that, and it doesn't look like the dragons are going to declare war on the ponies anytime soon. The Crossover tag is for the return of some pastiches of Invader Zim characters that I've used before.