Coverart by http://xn-dragon.deviantart.com
Trigger Warning: The word "Anonymous"

Some three centuries after Twilight Sparkle's coronation, something stranger than anything in Equestria's history appears in the very heart of Equestria itself. A human, lost, confused, and alone, finds himself warily welcomed by the rulers of this strange land.
After trading information about himself for information about the world he'll soon call home, he leaves from Canterlot to the quaint and quiet town of Ponyville, where he eventually meets a lonely bat-pony by the name of Speck.

A rewrite of the original ( http://pastebin.com/u/NukePone ) with additional content, restructuring, and fixes.
Featured from 09Jun14 to 12Jun14
Repeat feature nearly every time a new chapter is posted.

It has been several months since the disappearance of Twilight Sparkle..

One night, after watching her sister raise the Moon and set the heavens alight, Princess Celestia begins to bed down for the night, only to be interrupted by portal forming in her room. From out of the portal comes none other than Twilight Sparkle, garbed in strange armor.

Princess Celestia, along with Luna, Cadence, and Shining Armor, are overjoyed by the Element of Magic's return, but are justifiably curious as to where she had been and what she had been doing. And so, Twilight begins her tale. A tale of survival against impossible odds. A tale of a people fighting for the most basic right of all sentient beings. The right to exist.

In the frozen north of the Equestrian Wasteland lays a city, battered and crippled, but still clinging to life. It is beset on all sides my dangers.

Displaced griffins rage against the ponies they blame for the apocalypse. Madmares brood with their unquestioning minions under mountains of prewar technology. The Unity extends its malefic tendrils to sake it endless hunger for slaves. Unnatural horrors stalk the forests, consuming all in their path. A dozen factions rage against each other in wars of words, caps, secrets and fire, tearing at the very foundation of The Sovereign City. All the while an ancient threat prepares to once again, bathe its self in the blood and anguish of ponies.

Welcome to Flankorage.

(Comments are encouraged as this is my first attempt at fan fiction. The more feed back I can get, the better I can write.)

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.