It has been ten years since the defeat of the Changling Queen, and Equestria is again at peace. Twilight Sparkle and the Elements of Harmony have reached their prime, and have begun to settle down. Love and life abound in Ponyville, especially for Twilight's friends, but she has nopony to call her own.

There is a reason.

A series of events lead to a horrible revelation, and Twilight is thrust deep into a terrifying web of secrets and lies. Her peace is over.

This time, however, she won't be fighting monsters or madponies. What she faces will be much, much worse.

Act One of Two.

Act Two is here.

Currently undergoing editing by the wonderful Mstar!

Not quite a mare, but unhappy being a colt. It's a hard position for a young pony to be in. Would be easier if judgement weren't in every look, hate in every scowl. For Glitter Shell, even her friends and family aren't giving her the support she needs. So, she goes to find some in her personal hero.

Based on the blog Ask Glitter Shell. Give it a chance; I doubt you'll regret it.

Featured on Equestria Daily on August 12th, 2013; thank all of you for the support! Though please remember to support trans people in real life. This story is a very tame snapshot of what they have to go through for most of their lives.

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

This story is a sequel to The Secret Life of Rarity

After the events of The Secret Life of Rarity, Sweetie Belle must find a way to cope in a world that she does not understand anymore.

There is a threequel too.

Now with a TVTropes page!!!

Cover art by the wonderful Viofriedsebe

Daring Do has never turned away from a challenge. But when she finds herself trapped beneath an ancient temple with a haunted artifact, she may end up wishing she'd stayed home instead.

First place story in the Equestria Daily 2013 Nightmare Night Contest!

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.

Prince Blueblood thought the Grand Galloping Gala was over. He thought he could just go to sleep and put it behind him. He never expected to be reliving the same disaster of a day, over and over... and over.

TV tropes page here:
http://tvtropes.org/pmwiki/pmwiki.php/FanFic/TheBestNightEver

Thanks to all the people who wrote the page and all the people who gave me a little wakeup call and comment to become aware of that fact! You can't see it, but you guys put a real smile on my face tonight.

Also, recently, extra thanks to RD Dash for giving TBNE a thorough editing. I've updated the fic accordingly (7.11.12)

This story is a sequel to Lines and Webs

For four long years, Celestia's apprentice Twilight Sparkle, once a model pony and a hero among heroes, has waged a bitter and secret struggle with her onetime mentor. Though she works from the shadows, directing her forces from the Old Capitol in the Everfree Forest, Twilight Sparkle is unable to gain any advantage,

Likewise, Princess Celestia finds her once-faithful student far more cunning and elusive than she had anticipated, and even now searches for a way to bring Twilight Sparkle's rebellion to its knees.

It is a game of greys, of knives in the dark and of poisoned wine, where pawns are moved and traded and exchanged for greater advantage, all the while drawing both sides nearer to the conflict which shall tear Equestria in two.

At the center of this conflict is a new pawn, one who only wished to see the truth for herself. Drawn into a deadly game whose rules she does not understand, Sweetie Belle must learn to survive in a world where all is darkened, and nopony can be completely trusted.

Because when gods play chess, all pieces are expendable.

A nation will crumble, old enemies shall return in the most unexpected ways, and regardless of who is victorious, only one thing can be certain.

Nothing shall ever be the same.

Followed by Stormsinger.

Caught in the middle of a struggle between Equestria and a neighboring country, Blueblood finds himself alone in unfriendly territory. Through trials and hardships he finds himself under the wing of a veteran soldier, and the arrogant, spoiled stallion begins a slow metamorphosis into the prince his country needs.

The following transcripts are of a journal found in Ponyville on April 16th of this year. The last recorded contact with the town had been 3 days prior, on the 13th, when a team under orders from Princess Celestia was sent to look into several missing pony reports in the area. When another group of investigators were sent on the 16th, the town was found deserted. The journal’s owner is believed to be the princess’s personal student, Twilight Sparkle. None of the town’s inhabitants have been located in the weeks since.

Readings:
Nimbus Productions
Scribbler Productions

I highly recommend both of them.

A print version of all the stories in this series can be found here.