*Under Construction*
I AM changing the previous chapters instead of doing a full Revoke. I have read others work and feel that I can make it better.
Princess Twilight Sparkle has been tasked with exploring the ruins deep in the Everfree Forest. What she didn't realize, is that there is more to those woods than just scary trees, timber wolves and unpredictable weather. The woods are also the home of a long forgotten race.

Who are they? Why do they live there? And what does it have to do with Princess Celestia and Princess Luna?

History hints at their existences, foal stories talk about their magical ways, yet that is all: just stories.
What are they really? Do they even still exist? And what is their connection to Celestia and Luna?

It turns out: There is a Queen of the flutter ponies. She has been secretly hiding in Equestria for well over 2000 years. She is kind, benevolent, wise and imortal, just like Celestia and Luna. So why is she incredibly bitter?
She rules in shadows, in a land without rules.

On the eve of her cornation, Princess Twilight Sparkle will seek answers to unknown mysteries, along with finding a new home. Will she find what hides and bring it into a new age, or will the past remain hidden in the depths of the Everfree.

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

After an uprising against magic by the Pegasi and Earth Ponies, all unicorns- and all magic have ceased to exist. The sun and moon sit motionless and the stars no longer shine, creating eternal twilight. However, one spark of magic remains; hidden in a young unicorn filly, the last of her kind. Her destiny may hold the key to returning magic to all of Equestria. But she can't do it alone and will need the help from a few unexpected sources to bring back the magic and the stars. The question remains, is Starlight up to the challenge?
*Set in the future, about 15 years after the events in the show*
*Disregards all Season Four events and is cannon accurate up to and beyond that point as if Season Four didn't happen*
Cover Art is made by me with a base by Softybases http://softybases.deviantart.com/

The wheel of time turns, as destiny and history clash together.

Fifty years into the future, Sunset Shimmer is Princess Twilight Sparkle's most faithful student. She is smart and eager, but doesn't always think things through. Her life had been perfect, right up to the End of the World.

With a ruined future, Sunset travels into the past to alter the course of history. With only her mentor's cryptic word to go on, Sunset and the Elements of Harmony must solve the riddle of the Dark Regalia and stop the mysterious Vesper Radiance from rising to power. But the further Sunset goes, the more she feels like she's been through it all before.

Is destiny set in stone, or can Sunset shape her own future? Only time will tell.

Featured on Equestria Daily 6/16/13
Gratefully edited by JustAnotherTimeLord, Icarus_Gizmo, Cerulean Voice and Bad_Seed_72

The Sunset of Tropes page!

WANTED:

The newly crowned Princess Twilight Sparkle has set up a bold new initiative to discover new magic, and is sending out an open call to the unicorns of Equestria to apply for her research team. No experience in magical theory or research necessary. Enthusiasm and out-of-the-box thinking a must. The Equestrian government is not responsible for any physical, emotional, or magical trauma experienced during the course of the project or the application process.

Cover art by Page Turner

As a filly Celestia was not destined for great things. She was a slow learner and mischevious. Her younger sister Luna however, she was destined to rule and one day become a god. The traditional offering of one Allicorn foal to the Star of Stars was about to happen. When Celestia is put in Luna's place by mistake the star takes Celestia on a journey to godhood. Now hundreds of years have passed. The Alicorns are gone and there are no suitable offerings to give to the star. Celestia must choose from her subjects which pony is to be given to the star and take the place of their benevolent ruler.

The Trial of The Champion is a time honored event between Celestia's Sun Guard and Luna's Moon Guard. The event is used to remember the founding events of their forefathers who had guarded the princesses long ago. This year, however, two newly formed regiments have been allowed to compete in the week long events. Princess Cadence's Legion of the Heart and Princess Twilight's Witch Brigade.

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?

At first Twilight thought that being an Alicorn was amazing, but then her friends continue to age around her as she stays the same.

When Rainbow Dash unleashed the first Sonic Rainboom she created a magical connection between the Mane Six, starting them on the path that would lead them to defeating the most dangerous evil villains Equestria has ever faced as well as mastering the magic of the Elements of Harmony. However creatures loyal to those defeated by the Twilight and her friends travel back in time to change the past, all of time since rewrites itself. Will Twilight be able to reunite with her friends? And if she is, how will they be changed in this world of shadows, this world of madness, this Nightmare Equestria.