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!

After a week of recovering from her return Princess Luna seeks to return what was lost by her banishment and find the one pony she cares for the most... her daughter.

This is a rewrite of my old story. I hope you like it

Twilight Sparkle is changing; she's not sure how, or why. All she does
know is that she has to reverse the change before she hurts somepony she
cares about. But she won't be alone, Spike will be by her side until the
end.

"What a shame she wasn’t here to see this. She would have been proud. Yes, happy to see her faithful student taking her throne for her own, corrupted power. What a faithful student she was."

Short story.

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

King Sombra came from an old age, a time where darkness and evil were prevalent across the land. The Princesse's power and influence were weaker in those days, for the land of Equestria was divided amongst many kingdoms of lesser Princesses and Princes. But out of all their ruling neighbors, The Four Shepherds held the most power of all, even threatening Celestia and Luna's kingdom. However, all of that changed when they vanished for a thousand years, ushering in a new era of peace and prosperity. Until that is, when the Crystal Kingdom reappeared, along with one of the Shepherds. King Sombra, however, was thankfully vanquished swiftly, but the following peace of his defeat would not last as long as anypony might think. A new force sets its eyes on the recently coronated Princess Twilight Sparkle, one that seeks to restore a lost heritage and remind the land of who is the true owner of the night. For when one evil is smitten, another appears in its place. And King Sombra was only the first in line.

Set before Season 4

Note: Dark tag is meant for Light Dark

Special thanks to my editor Ladrian for his diligent and superb work. I wish I had him when I first started this story because maybe then the early chapters would have been much better.

Special thanks to Stanku for revisions and prereading this story. It would be at a much worse state had it not been for his detailed opinions to each and every chapter, and letting me know where I can improve.

10/2/2014 : Woah... it's on the featured list... *cue squealing and fist pumping* THANK YOU ALL SO MUCH!

(REWRITE IN PROGRESS)

After a weekend spent in Canterlot, Twilight Sparkle arrives home to find an odd scroll in her saddlebags. In the following days Twilight is plagued by terrifying nightmares, and horrific visions from a life not her own. Can Twilight Sparkle resist the Nightmare, or will she fall prey to the darkness?

We trained her.
We taught her.
We raised her to godhood.
She brought us down to earth.

Sequel can be found here: Memoirs in Ink and Blood

For a thousand years, the Code of Harmony has ruled Equestria, and the Code of Dissonance has sabotaged its works at every turn. Now the war for control over the land will come to a head, and one unicorn's decision may decide the fate of all.

For though she does not know it, Twilight Sparkle is the shining example of the Code of Harmony. Her teacher, Princess Celestia is Harmony's most powerful master and she knows her enemies are hatching a plan that threatens to cast down the Harmony of her throne and all she has sacrificed to create.

What she does not know is her foe seeks a new Apprentice to turn to his dark ways. A unicorn with seemingly limitless potential for magic, whose thirst for knowledge may yet lead her down a dark path, who is known to be such a faithful student of magic, eagerly seeking the truth no matter how forbidden it might be...

Sequel: Code of Harmony

Some things in this world happen by chance. Others do not. Twilight Sparkle is about to learn a disturbing truth that will turn her world upside down.

- Originally written May 2011 for Deviant Art

Reading this story first is strongly recommended:
(Blood is Thicker) http://ciroton.deviantart.com/gallery/26378692#/d3e1ndq

Credits:
~Image by JohnJoseco~ ~Edited by BrotherPrickle on Deviant Art~