The Sequel to Number 12.
The Doctor and Twilight leap into the future, though it may be a far darker place than they envision. In the mean time somehow the Doctor keeps crashing around Ponyville, something to do with Fluttershy, but what?

A blue box has fallen out of the sky, and crashed right into Twilight's Library! A strange brown stallion, calling himself the Doctor stumbles out. Soon after, strange stone Pegasus are everywhere, one of resident weather ponies has vanished, and Twilight is tossed in the middle! The Doctor and Twilight have to find out what's going on, before it's too late!

Twilight Sparkle is summoned to settle a legal matter involving The Great and Powerful Trixie... What in Equestria did she do now?

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

Set in the far future after Celestia and Luna mysteriously vanished and the sun and moon froze in the sky, Antipodes is the story of two ponies thrust out into the harsh new world on an adventure to uncover what happened to the world so long ago.

(I wrote this when I was 17. it's pretty rough in places, but i think the basic ideas i had here were pretty cool. it's got a good skeleton)

Spanish translation here: https://www.deviantart.com/spaniard-kiwi/art/Antipodas-1-3-953524835