Twilight Sparkle had been looking forward to a quiet, relaxing day with a friend, and at first it seemed that Fluttershy could provide just that. But when Twilight makes a rather unsettling discovery about the pegasus – and her unusually sanguine appetite – the knowledge proves to be anything but relaxing...

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

After a mysterious and widespread spell causes ponykind to vanish, Fluttershy is left behind to cope with what the future has in store for her and the remains of Equestria.

In a matter of days, the once-prosperous nation begins to descend into a harsh and unforgiving place. While cities crumble around her, Fluttershy finds herself living in a land rife with dangers and heartbreaking reminders. With nopony to turn to, Fluttershy is forced to learn to fend for herself, discover what happened, and, if possible, find a way to reverse it.

Survivor Shy is an illustrated story following Fluttershy in the weeks after a magical cataclysm. While the last pony relives her past, readers are offered a vivid glimpse into Fluttershy's mind and are led on a harrowing journey through the ruins of Equestria and beyond.

Story branches out before Season 3 Finale.

In-progress Reading by Finish Line available
In-progress Russian translation by Papilion_star available.

Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

A refined mare fresh out of high school and a dropout following her dreams find themselves forced to spend a lot of time together.

With the help of a meddling psychology tutor and their new classmates, can they find what they've been looking for?

French Translation!

Fan Stuff!

This story is a sequel to Discordant

Almost ten years have passed since Scootaloo helped free Discord. She’s learned to live with the consequences, but it’s never easy. After being fired from the local weather control team, she receives a letter from Princess Celestia, offering her a job as an assistant flight instructor for gifted pegasi. With no better options, she reluctantly accepts. But why her, what game is Celestia playing, and what exactly is going on in Canterlot?

Distance can drive us apart. It can also bring us closer together.

After all is said and done, and the ponies have gone their separate ways, the only way they have to keep in touch is through letters.

Original Equestria Daily post is here
Russian translation
Chinese translation
Polish translation
Spanish translation

Now with music and audiobook

After Big Macintosh helps the Mane Six out of a jam, he finds his ordinary life of
peaceful routine thoroughly disrupted by the various misadventures those crazy
ponies always seem to get themselves into.

Artwork provided by the talented Zemious

Mort, also known as the Pale Pony (of Death), has been tasked to take time off from his rigorous duties of reaping souls. Seeking guidance, he is directed towards the town of Ponyville, to learn about the magic of friendship from Twilight Sparkle and her friends. All he needs to do is keep his true nature a secret. That shouldn't be too difficult...right?

Special thanks to Specter-Von-Baren and Pyrite Foolsgold for their help in proofreading and editing this story, as I really needed it. Additional thanks to Pilate, Chuckle5, Unimpressive Vagaries and Admiral Biscuit as well! Couldn't have done it without all their help!

Credit for the title card goes to Siansaar, AKA Carnifex.

For another excellent take on Mort, check out Sip's version!

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!