Empress Moon!

Broken on the Wheel Trixie lost everything to the Alicorn Amulet. But, after Trixie is tricked into becoming the new host of the Nightmare, she is the only mare who can save Equestria from eternal darkness, if she wants to. by billymorph 26,733 words · 122 · 6
The Moon's Apprentice Twilight Sparkle failed her entrance exams for Celestia’s school. Worse, she is a danger to both herself and others, resulting in her magic being suppressed. Dreams crushed and now one of the weakest unicorns, a nightmare comes to her. by Forthwith 412,134 words · 3,779 · 169
Twilight, Revised Twilight Sparkle gets brainwashed. Mind controlled, sort-of Twilight x Celestia. Nightmare Moon too. by An Unimpressive 33,727 words · 897 · 80
The Mare Who Once Lived on the Moon In a steampunk reimagining of the universe, Twilight Sparkle finds perhaps the one pony as lonely as she is. It's rather unfortunate that they're on the moon. by MrNumbers 143,130 words · 3,008 · 57

More Empress Moon!

Night's Favoured Child With her new apprenticeship under Nightmare Moon, Empress of Equestria and Queen of the Eternal Night, the orphan filly Twilight Sparkle plunges head-first into the conspiracies, secrets and intrigues of the Empire. by Municipal Engines 151,320 words · 3,757 · 62
Mare Doloris It was the perfect moon for a hermit, except for one little problem; I wasn't alone. by TinCan 59,513 words · 198 · 4
The Devil's Trick As the details surrounding the Canterlot Invasion don't add up, Twilight investigates the suspicious disappearance of a guard during the attack. Just how did Chrysalis manage to sneak so deeply into their ranks? by Soundslikeponies 3,318 words · 631 · 19
The Lies We Tell to Children When Twilight is awake, Celestia is her teacher, and she a faithful student. But when Twilight shuts her eyes, another mare approaches, who teaches her a very different lesson. by GaPJaxie 37,144 words · 906 · 30