A heated confrontation with Celestia over her portrayal as Nightmare Moon and her sister's authoritarianism leads Luna to search for answers about the past, unwittingly tangling Twilight and her friends into a cosmic struggle between order and liberty. The tragedy of the past bleeds into the present as the Royal Guard, led by the (in)famous Captain Braveheart, pursues the moon goddess as if the fate of the world depended on it. A tale dedicated to the history and government of Equestria, the psychology and political/moral philosophy of the characters, and especially that amorphous and mysterious force that so many seek yet so few gain: power. What is its nature, what drives us to pursue it and keep it? What does it mean to be a leader, a princess, or a goddess at that matter? These are but a few of the questions the characters must struggle with in order to restore harmony to Equestria. This story tries to bring an edge of realism to the political organization and history of Equestria. If you're seeking utopia or dystopia or extremes of any sort, it's not here. .

What if the villains were allowed to win without a fight? Would all of their plans bear them the fruits they so desired?
Probably not, especially when their royal adviser is Twilight Sparkle.

A collection of (continuous) One-shots in which our heroes don't have any epic fights with villains, and simply allow the power of logic to crush all of the hopes and wishes of the would-be rulers of Equestria.

Currently up: Nightmare Moon, Discord, Chrysalis, Sombra (bonus chapter - the fight is so not-epic it happens off screen).

Princess Celestia’s School for Gifted Unicorns is famous across Equestria as a center of academic excellence. Only the best and brightest unicorns are offered places, selected by their academic merit, magical ability and passion for study. To make the admissions process as fair and reliable as possible, all candidates are given three exams by different teams of examiners, who then meet in private to decide which students are most deserving of a place.

Winner of the December 2014 Writeoff competition: Behind Closed Doors.

Princess Celestia has been keeping a dark secret from her subjects for a very long time.

It's not an easy truth to tell, but if anyone can accept her after learning it, it will surely be her most faithful student.

Third Place Finisher in Equestria Daily's 2013 Nightmare Night Contest!

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

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

As a descendant of the greatest conjurer of the pre-classical era, Star Swirl wishes to live up to her namesake's reputation and their shared cutie mark. But how can she emulate a powerful unicorn when she is an earth pony? Taking the advice of her psychologist, she heads off to Ponyville to try and find out. (Image property of Cybertoaster) (Now the first in a series)

Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

An aspiring rationalist gets punted into Equestria - and instead of being turned into a cool griffon, or powerful dragon, or even a standard pony... discovers he is now a milk-cow, part of the herd.

Part of the Chess Game of the Gods crossover.