When alternate universe versions of Lauren Faust and Craig McCracken living the high-tech future of a dying Earth become the victims of a raid by the Ponification for Earth's Rebirth group, their lives will never be the same. The lives of everybody and everypony else in both Equestria and Earth will be forever changed as well as Lauren, Craig, and a mysterious newcomer join the Mane Six in both trying to fit into a new life they didn't choose and discovering an ancient conspiracy that holds the truth behind The Conversion Bureaus and everything connected to them. What started with an anomaly will end with a revelation that could very well destroy both worlds.
(Seperate from The Animation Bureau alternate universe)

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!

The tyrannical Shadow Stallion oppresses Equestria, coating the land in a thick layer of clouds, tightly controlling the population. Three children, the unicorns Celestia and Luna, along with a Draconequus, Discord, must live up to their fate. They must find the Elements of Harmony and take up their rightful place as Equestrias new gods and saviors.

Adventure and Friendshipping mix, intended to be a possible prequel to the show. Featured on EqD since January 09, 2012. Six Stars.

Nine months was all it took for one earth pony to put Princess Celestia on the defensive. A fledgling protest movement and its wily leader have risen to challenge both her and Luna's age-old rule. And though Celestia harbors many doubts about her adversary’s true motivations, she can't shake the feeling that her own frantic strategy to restore order just might be proving the protesters’ point. As she and a devoted Royal Guardspony race to tamp down the flames from Just Cause’s torch, the princess will discover firsthoof what happens when her sister’s regrets and resentments are set free, when the loyalty of Equestria’s bravest is pushed to its limits, and when a few ponies’ genuine fears are ignored for just a moment too long. Featured on Equestria Daily!

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

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

There comes a time when the light must go out; but how do you know if you've burned brightly enough?

Night and day. Fire and ice. Creation and destruction. Everything has an opposite, and Chaos is no exception. Princess Celestia tells Twilight the true history of Discord's rise, the Alicorns' fall, and the creation of the Elements of Harmony.

She tells her student the story of Order and Chaos.

‘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...

Twilight can not find her pillow.