After Minuette receives her hourglass cutie mark, she must join Equestria's mysterious and secretive Order of Timekeepers, the worshipers of the Titan Chronos doomed to count the hours, minutes, and seconds of every day to ensure the princesses raise the sun and moon on time. But when Queen Chrysalis begins snatching chronomasters from across Equestria, it's up to Minuette and the last remnant of the Order to stop her. With changelings at every turn, there is nopony they can trust, yet only trust can save them.

Now with its own TVTropes page!

Featured by Seattle's Angels.

Translated into Polish by Korodzik.

Thanks to adamscage for the cover art.

Part of the SALT September 2012 writing contest.

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.

[Complete] Celestia awakens to see an empty world, white sandstone stretching the horizon. She wanders the world as she builds it from her imagination, filling it with life, but as time passes, the world that she created begins to seem like little more than a lucid dream, conjured from the dust.

Derpy Hooves is secretly a changeling.

Nopony particularly notices, or cares.

(New 9/15/19: Spanish translation by Spaniard Kiwi! Thank you!)

"YOU ARE NOT THE REAL PINKIE PIE!"
"You probably shouldn't even exist."
"You're only a clone, you don't HAVE any feelings!"

Who was she to believe? She was barely a day old, and already she'd seen the disappearance of her mirror images, all but her. Was she just a clone? A disposable unfeeling analog?
What would happen if she became her own pony? If she became real?

Is it possible for one of the Pinkie's, the only copy left behind, to develop? To become an entirely different pony to the one that she was modelled after?

Oh, and before I forget, thanks to the amazing WerewolfNobody for the (At one point) cover art!
Featured on Equestria Daily!

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

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

Immediately following the events of Appletheosis, Applejack must relearn her place in the world as the new Princess Mara of Equestria. Meanwhile, her family and friends have their own troubles with the changes. Through it all, little Merry May, first in the service of her goddess, tries to hold things together and keep everypony sane and happy.

I won't tell you what to do, (this time) but reading Appletheosis first is highly recommended. The Shadow of the Goddess also provides useful background and will become very relevant in later chapters.

This story is a sequel to Steel Soul

Sweetie Belle has discovered a secret. She's spent a few months keeping it to herself, but the nightmares she's had have convinced her it might be time to reveal it.

Sequel to Steel Soul.

Why, hello there! Can't say that I've seen you around before. Welcome to Ponyville Library. Let me know if you need help with anything. Oh, right. Where are my manners? My name is Twilight Sparkle, personal student of Princess Celestia of Equestria and resident librarian. Oh, and some might call me the laziest unicorn in Ponyville.

Heh. They're just jealous. Try the laziest unicorn in all of Equestria. And that's a title I'm most proud to bear, thank you very much. What's that? Why, you ask? Well. Let me tell you about the time that I accidentally managed to save Equestria.

Several times, actually.

Note: Not a crossover with "A Series of Unfortunate Events." Sorry to disappoint. I just couldn't resist the reference.

First person from Twilight's perspective.