First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

Talks broke down. The unification failed. Hearth's Warming have never occurred. The Great Pony War divided the land, and fears of a prophecy forced the unicorns deep underground and into near extinction.

Almost one thousand years have passed. The curious unicorn Sparkle yearns to breach the surface to discover its many wonders and to search for her missing father and brother, both of whom crossed over many years ago. She is forbidden to leave the safety of her subterranean village of Unicornia until she discovers an orange earth pony washed up on the shores of an underground river. That pony bears one of the six Elements fabled to change the world.

Or destroy it.

Cover art credit goes to ouyrof.

Re:Harmony was conceived before Season 4 aired, so some personalities and character relations do not line up with the show's canon.

Also, please refrain from revealing spoilers in the comments. Thanks!

The Ponyspawn have invaded Equestria, and it is up to the newest addition to the Grey Wardens, Twilight Sparkle, to find the means to drive them back! With her friends and allies at her side, can Twilight defeat the evil tide before all of Equestria is devoured?

The Sequel, Pony Age: Catalyst, is available.

Art by ss2sonic. Check him out!

Before he left, Spike make a horrible mistake. He told all of his friends that he would leave Ponyville to cleanse the demon within him and to make amends for the suffering he brought. All of his friends didn't want him to leave, but he made up his mind. He said farewell to his saddened friends and painfully walked away from what he called "home". He told himself to venture of to the "Cavern of Greed". There, he can fight the demon from within...

5 years after the incident and all is peaceful in the town called Ponyville. Not a frown to be seen; not a cry to be heard. All was calm till a mysterious cloaked stranger came to the peaceful town. All the noise; all the chattering ceased. The stranger walked until he was in the middle of the town and simply said, "I'm home".

(Each chapter will be someone else's POV. The story progresses as the chapters go on. Also, come to this blog. I'd like to ask a question.)

Editor: LightningBass94. I can't thank enough without him(her) because my english is somewhat bad….

For almost a thousand years, the immortal Nightmare Moon has reigned over Equestria as Empress. To the average pony, Nightmare Moon is an overarching enigma whose rule is absolute and whose wrath is terrible. But to Twilight Sparkle, who as an orphan has never known her parents, the Empress is something else entirely. When the young unicorn is brought under the royal wing as an apprentice, she learns a great deal more about the supposed tyrant than she ever knew. But as Twilight is introduced to life with her new mentor, she is thrust into a world of political intrigue, conspiracies and secrets. Secrets that were never meant to be revealed. As allies and enemies plot against the very peace of the nation, will Twilight fall prey to the perils of her new position? Or will she prosper and find in Nightmare Moon the mother she never had?

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My eternal gratitude to my editor, LordOfTheWrongs, without whom Night's Favoured Child would not be the story it is today.

Now with added TVtropes!