Night's Favored Child

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?

Night's Favored Child is a My Little Pony: Friendship Is Magic fanfiction by Municipal Engines, who is assisted by LordOfTheWrongs. It can be read here or here.

Tropes used in Night's Favored Child include:

Alternate Universe Fic: Nightmare Moon triumphed over Celestia in the backstory.
Black Cloak: The defining article of clothing for the Imperial Overwatch - so much so that they are nicknamed the "Blackcloaks".
Conveniently an Orphan: Twilight Sparkle
The Bad Guy Wins: The result of the historical fight between Nightmare Moon and Celestia.
The Brigadier: Marshal Silverstar
The Empire: What Equestria was turned into with Nightmare Moon at the helm.
Enigmatic Minion: The Inquisitor is this in spades. Just how enigmatic is he? Well, for one thing, Nightmare Moon doesn't remember when he started working for her -It's like he's been there from the beginning. But more than that, he knows Nightmare Moon is Luna.
Everyone Calls Him "Barkeep": The Inquisitor
Interfaith Smoothie: The Enlightened Way blends the trappings of Christianity, Islam, and Buddhism.
Psychotic Smirk: The Inquisitor has a good one.
The Empress: Nightmare Moon is referred to as "Empress" rather than "Princess".
Evil Chancellor: The Inquisitor is one of these. Probably.
Last of Her Kind: The relatively recent religion surrounding Nightmare Moon labels her "The One [Alicorn] Who Stayed".
La Résistance: Mostly in the background so far, but Twilight's parents were members.
The Spymaster: With the Overwatch at his command, the Inquisitor acts as head of intelligence and internal security for Equestria.
Written by the Winners: In Nightmare Moon's Equestria, history has been altered and edited to wipe out knowledge of Celestia and her day, to the point that words like 'dawn', 'sun', and (notably) 'twilight' are eradicated from the Equestrian lexicon.
Victory Is Boring: Nightmare Moon admits that the joy of being revered and worshiped faded after the first century or so.