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.

Bon Bon's voice is funny, and that's about all that anypony who meets her notices, as her marefriend Lyra soon steals the spotlight with her explosive personality, strange obsessions, and curious beliefs. And why not? Bon Bon is, after all, a perfectly ordinary, boring pony in every way but two: her voice, and the carefully kept secret that she isn't really a pony.

(Edit:) Now with an annotated version, courtesy of the incomparable Shoggoth Lord!

Twelve thousand years ago, humanity was driven into a war with an unknown enemy. Fire rained from the heavens and the sky turned dark as the sun dimmed. Acid poured from the clouds and a plague was unleashed upon mankind: A virus that caused men to turn on one another. A disease that forced man to fall to his knees and beg for mercy. A pathogen that ravaged man’s civilization.

And when humanity lost all chances of reconciliation, all hope of keeping their loved ones safe, they pulled the plug, three hundred souls left Earth while sacrificing their only home to the angel of the enemy.

In the twelve millennia since the Great War, all traces of humanity have been wiped from the surface of the Earth. In man’s rightful place now are a multitude of sapient species. For twelve thousand years, these animals have lived in peace and harmony, man reduced to nothing more than but a myth, a folk tale, a legend.

But word has spread across the countryside. Word of forgotten beasts that still walk the western wastelands. Creatures able to bend the world to their will without the help of magic. Creatures said to be older than time itself.

Teen for language, and dark moments. Character tags will be added as the story progresses

Takes place in an alternate universe where Celestia and Luna used the Elements of Harmony to slay King Sombra.

Celestia and Luna are no more. The sun and moon have collided, and the heavens torn asunder in the aftermath of their final battle. The Elements of Harmony are missing, presumed forever lost. The fiends of Tartarus are on a rampage, and no one can stop them. And to make things perfect, the ruler of the nation of Boardor has decided to invade.
Desperate, Clover the Clever's last living student gathers together 108 virgin mares, in order to perform a ritual that will revive King Sombra. They succeed... kinda.
A human, in King Sombra's body, suddenly finds himself in an Equestria in a downward spiral with a bunch of technicolor ponies begging him to save them. Convinced that he's either dreaming, stoned, or insane, he tries to go along with it as best he can, although the voice in his head, a very angry voice with a hunger for conquest, crystals, slavery, and stairs, isn't doing much to instill confidence in his own sanity...

New Cover Art By Shadow Bolt!

This story is a sequel to Project Sunflower: Harmony

In every tale, there are unseen details. Small stories, often going unnoticed. This is a collection of those stories that relate to Project Sunflower: Harmony.

It isn't recommended to read these stories without reading the main story. Without the context provided in Project Sunflower: Harmony, it isn't likely that these chapters will make much sense.

Every chapter will have an author's note detailing where it fits in the main storyline. These chapters are intended to be optional to read, and are intended to add some depth and color to the main story.

Cover art by Genbulein

This story is a sequel to Stormsinger

In wake of the assault on Starfall, Serale Everstar has agreed to her mother's wishes, and will travel the length of Equestria to pay respects to her mother's rival Courts. But burgeoning magical ability and the possibility of traitors around every corner have placed on the young Lady more stress than she could hope to bear alone.

Apprenticed to the Court Mage, Cobblestone, recently a cutpurse and recovering addict, is eager to begin her training in the arcane arts. But her own abilities have attracted the attention of old powers, not all of them with her best interests at heart.

Tasked with protecting his Lady at the cost of his honor, Vino Hedera is young and untested in the field of battle and the art of command. But all is not as it seems among his compatriots, and the greatest danger he faces may well come from within the ranks of those he should be able to trust with his life.

With the forces of the Shadow gathering, pursued by forces both foul and Fae, and unsure of who to turn to, these three ponies may have only each other to rely upon in the face of the most terrible enemy Equestria has ever known. It falls to them to prepare for oncoming war, one in which the stars may shake and the sun itself may fall from the sky.

Book Four of the Sunfall Saga. Book Three to be found here.

It has been one of the closest guarded secrets of Canterlot's royalty. Deep in a specially constructed dungeon, surrounded by warding spells and powerful magic barriers, exists an enigma. Within a cage that could only be described as something out of a nightmare, it waits and watches all of Equestria. A creature that cannot age, is immune to disease, does not thirst nor hunger, and resists all injury. But, it also holds secrets and knowledge that could safeguard the kingdom. Its powers are frightening, but it is civil enough for debate when patience permits.

Princess Celestia has sought counsel with the creature before, enduring it making deal after deal for its services. The Princess walks a fine line when dealing with it, knowing full well anything could give it an advantage despite its imprisonment. She has had to go back on her word in these dealings, and from this a deep animosity between them has been born. It is a necessary evil as she is convinced this is a being capable of untold evil far and above anything Equestria has ever dreamed of. So long as it remains within the confines of its cell, her kingdom is made safe. So much magic has been woven to ensure that, there is little chance of escape.

So long as the magic holds, there is no danger. So long as the cage remains strong, the nameless creature stays enthralled in his cavernous dwelling. If that were to change--if the magic failed--not even the wisest could say. But one thing is assured, it does not bode well for Equestria.

(This is an old story I wrote three years ago during season 1)

Twilight Sparkle's birthday has come around, and Rainbow Dash is unimpressed with Rarity's present. When Applejack pokes a bit of fun with her friend, Rarity becomes unusually upset. Twilight Sparkle investigates her friend's feeling, learning something she never expected about her friend and why she is truly suited to be the element of Generosity.

Spanish translation: https://www.deviantart.com/spaniard-kiwi/art/Simply-Rarity-Spanish-translation-846034960

After a tragic accident, a human ends up in Lord Tirek's body, as part of an attempt to reform the villain after his recent escapades. While the hero of our tale is trying to make sense of his new surroundings, the rest of Equestria thinks that the most terrible threat that their world has ever seen is back...
And the powers that be are definitely not happy about it.
New Cover Art By Shadow Bolt

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.