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. 

Was it a magical spell gone awry? An angry god laying waste upon a world that had forgotten him? A long and bloody war? An incurable disease?

Fluttershy couldn't remember what it was that had turned the world to this. All she knew was that she had to survive.

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.

Over the course of several years, Rarity has achieved a fabulous career, contributing to both Equestrian fashion and the Ponyville community. She is admired by her clients, envied by her peers, and cherished by her dear friends, proving that she's a dependable shoulder to lean on.

Then one day, a mysterious pony visits from out of town. She wishes to meet Rarity, but not to thank her.

This is pretty much a self-insert, mostly done for comedic purposes.
After a mishap with an invention of mine, a friend and I find ourselves in the magical land of Equestria. How will the peaceful land of Equestria handle the influx of two humans? Will Jay and I ever find a way back home? Will anyone give this story a fair shot? Read and find out.
Things that actually involve MLP:FiM begin in the second chapter.

An alarm sounds. There's a planet nearby. I wonder if anyone can hear me.

Kuno, a young changeling, is left weak, bloodied, and bruised after the events of the Canterlot wedding. She is soon discovered by Warden, a Royal Guard. But for some reason, Warden shows her mercy. Instead of taking her into the custody of the Royal Guard, he becomes both her captor and her savior. But over time, Kuno will come to ask herself the hardest question she has ever pondered: Can a changeling feel love?

After the changeling invasion, the race of changelings is broken and scattered, their Queen mortally wounded. Extinction is inevitable, unless Queen Chrysalis can convince Princess Celestia and Luna into a desperate gamble for the survival of their race. Sometimes the only path to victory, is surrender.

Based off the video Children of Faust (not mine)

[Featured on EqD and FiM Fiction] Chrysalis is brought to Canterlot to stand trial for her failed invasion. Thinking her fate is sealed, she is determined to be defiant to the very end. Loosely based on March to the Scaffold, the 4th movement of the musical piece Symphonie Fantastique by Hector Berlioz.
All links to the music pieces are in the Author Notes.
Dramatic reading of the entire story by Illya Leonov
Dramatic reading of Chapter 1 by xPsychoShyx
Picture is by Huussii

War comes to Equestria: with despair, with starvation, with suffering and with sacrifice. And the ponies must learn how to keep true to their values while surviving not just the rigors of battle, but the desolation of total war.