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?

============

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!

Princess Celestia is a living legend, but much of her life is shrouded in mystery. Records have long since been lost to the decay of time, and the tale of her triumph over Discord has become a fable. The Princess's memory of the event has long since faded... or has it?

Her faithful student lending an eager ear, Celestia recounts the true story of a war-torn Equestria, the struggle against Discord, and the early years of her own life.

Before she was the Princess of the Sun, she was merely a stranger.

(Featured on Equestria Daily!)

The sequel to League of Discord. Twilight Sparkle and her friends have successfully returned the six champions to Runeterra, but find themselves dragged along with them. They must now find a way home, despite having no help from an apathetic League, and having yet another pair of ambitious and sinister eyes watching their every move.

This is an official End of Ponies side story, written with permission from Short Skirts and Explosions.

Red is a Diamond Dog that survived the cataclysm that brought about the end of Equestria. He lives in the Wasteland, operating a mechanic shop and airstrip. His life is simple; he spends his days working on airships and serving his pack. As a stormfront blows overhead, Red remembers a chance encounter with the Last Pony, and sets out on an adventure, determined to hunt down the last equine in the world.

It is not necessary to have read End of Ponies to understand Red Wings.

Twilight Sparkle, Celestia and Luna are transported into a strange alternate Equestria, the Land of Always Summer, where the day lasts forever and a terrible queen rules with an iron hoof.

Feel free to check out or add to the story's TV Tropes page.

A horrible Cataclysm has turned all of Equestria into a Wasteland of barren ash and twilight desolation. The Sun and the Moon have been destroyed. Everypony has died--including Princesses Luna and Celestia. But one pony miraculously survives; she is a lone wanderer, the last of her kind, surrounded by menacing creatures that hate her. She navigates the Wastes in an airship and scavenges off the blighted landscape to keep herself alive.

Then one day she meets an old companion who grants her a gift, the chance to go back in time to the warm and sunny days of Ponyville, where her dead friends live in happiness. How far will the last pony venture into this joyous age of Equestria, even if she fully knows that there is no way to change the horrible fate of everypony she loves?

2013 Edition: Smaller Chapters, Better Grammar, and a Few New Scenes

(A shout-out to Vimbert, pre-reader and gentlecolt)

After an unfortunate incident involving Rainbow Dash and herbal tea, Fluttershy wakes up one morning to discover that she has turned into a rabbit! With her friends unaware of her plight, Fluttershy must turn to Angel bunny to guide her on her quest to restore her original form. In the process, she is given the oppurtunity to experience everyday life in Ponyville from a whole new perspective, and discovers that there is much more to her friends' pets than she ever expected.

Cover art here if you'd like to compliment the artist: http://mischieflily.deviantart.com/#/d4wfix3

‘Have you ever,’ she started, ‘broken a promise you made?’

Celestia and Luna live a carefree childhood at Canterlot Castle, but its end approaches far too quickly — no matter how much they struggle, they find themselves drifting apart. And without their noticing, a new evil rises that could drive a wedge between them for good...

After Summer Sirocco's expulsion from the Royal Guard Academy, a captain of the Night Guard offers her an unexpected alternative. The choice: sacrifice her relationships and abandon her identity, or walk away from a singular opportunity to escape the pony she never wanted to be. It dredges up difficult questions of how she sees herself and who she really is—and her answers won't be easy either.

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim