It has been ten years since the defeat of the Changling Queen, and Equestria is again at peace. Twilight Sparkle and the Elements of Harmony have reached their prime, and have begun to settle down. Love and life abound in Ponyville, especially for Twilight's friends, but she has nopony to call her own.

There is a reason.

A series of events lead to a horrible revelation, and Twilight is thrust deep into a terrifying web of secrets and lies. Her peace is over.

This time, however, she won't be fighting monsters or madponies. What she faces will be much, much worse.

Act One of Two.

Act Two is here.

Currently undergoing editing by the wonderful Mstar!

Comet takes his job too seriously. Angel doesn't take anything seriously.

Comet joined to protect kingdom and princess(es). Angel joined for adventure and danger.

Comet isn't interested in mares. Angel can't stop talking about stallions.

Comet is a pegasus. Angel is a bat pony.

Together, this unlikely duo goes through life as Royal Guards from basic training to fully fledged guardsponies. Who knows? Maybe they'll even start to get along.

Cover art by slawomiro.

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

In a world full of magic, mere words can pose a deadly threat. When simply reading a sign can instantly infect the unwary, and cases start to turn up all around Ponyville, Twilight Sparkle casts the only spell she can find that can give her the time she needs to find the cause of the plague. But then she has to figure out how to stop the epidemic... without being able to read.

Editing provided by Spabble
If you like this, try Rainbow Typhoon
Audiobook on YouTube and for download on SoundCloud
Spanish version translated by MIkimoco
Russian version

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

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!

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