Recently rewritten. Contains occasional adult humor and violence.
***
On a request from Princess Celestia, Twilight Sparkle and the rest of the mane six explore an abandoned mansion located deep in the woods. While doing so, they unwittingly stumble across an enchanted mirror that scrambles their DNA and pops out three brand new bouncing baby ponies. Hilarity and drama ensue as the mane six must cope with being suddenly thrust into motherhood, as well as protect their new foals from a dark god that wishes to use them for his own sinister gain.

***

Fanart:
The three foals. by Freefraq on Deviantart.

This story is a sequel to Elementals of Harmony

A collection of stories set in the same Multiverse as Elementals of Harmony. Among other things, you will learn about Lyra's employers, how Equestria was made (really), and whether Luna snores.

A Friendship is Magic: the Gathering crossover, like its predecessor. Reading Elementals first is strongly recommended, as there will be spoilers.

Categories have been chosen in light of the wide range of tone.

This story is a sequel to My Little Alicorn

After the events of "My Little Alicorn," everything seemed to be back to normal...except for one pony. Prince Blueblood is now trapped as a colt, his title, possessions and birthright stripped for his crimes. Before Princess Celestia will return him to normal, however, he must prove himself by attending Magic Kindergarten. Even worse, his current situation has attracted the vengeful gaze of two ponies he has offended in the past: the Captain of the Royal Guard and the Moon Princess.

Will Blueblood rise above his past self and emerge a better pony? Or will he sink back into his old depravity, and be stuck a colt for the long term?

Note: This is a sequel to "My Little Alicorn," so you might want to check that out first.

How will a Pony adjust to living in your human apartment? More importantly, how will you adjust to living with a pony? A mare pony no less. You should have known that someone with the name of Fluttershy would have been a pony. Equestrian Ponies are just so... foreign! You never know how to act around them. Will you be able to overcome this and cope with this pony invasion into your life?

In part inspired/influenced by The Roommate by totallynotabrony.

In a world where she sees from a distorted perspective, all Twilight Sparkle can do is cling to the one pony she knows will never let her down: her teacher, the princess... no matter which princess her addled brain tells her that is. Twilight's used to rewriting letters, but when she's the one being rewritten, she finds the sensation to be altogether different.

Many thanks must go to my awesome editors, Varanus, Ebon Mane, shortskirtsandexplosions, Seattle_Lite, and Nick Nack.

Featured on Equestria Daily and The Pony Fiction Vault.
Check out/contribute to this story's TVTropes page!

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!

This story is a sequel to Of Solicitude

Ten years after a massive war, Equestria has changed. The Empire now rules over all, giving peace and prosperity to those that deserve it, but some are against this new rulership.
The CMC, a small, raggedy group of smugglers working for the Apple family, are caught red-hoofed by an Imperial patrol. As the friends fight for their lives, they learn about themselves, each other, and the world they now reside in.
Meanwhile, in Canterlot, Emperor Blueblood has amassed a massive fleet and is preparing to smash what is left of the rebellion under the oppressive hoof of his Empire.

Fantart:

http://www.youtube.com/watch?v=cSqZZHhQa_I

http://www.youtube.com/watch?v=JE7m2dk8FB4&list=UUS5YHp6kB61DHIXt8THr4iQ&index=1&feature=plcp

[Featured on EqD and FiM Fiction] Chrysalis is brought to Canterlot to stand trial for her failed invasion. Thinking her fate is sealed, she is determined to be defiant to the very end. Loosely based on March to the Scaffold, the 4th movement of the musical piece Symphonie Fantastique by Hector Berlioz.
All links to the music pieces are in the Author Notes.
Dramatic reading of the entire story by Illya Leonov
Dramatic reading of Chapter 1 by xPsychoShyx
Picture is by Huussii

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.

"My name is Lyra Heartstrings, and you will not remember me. You won't even remember this conversation. Just like with everypony else I've ever met, everything I do or say will be forgotten. Every letter I've written will appear blank; every piece of evidence I've left behind will end up missing. I'm stuck here in Ponyville because of the same curse that has made me so forgettable. Still, that doesn't stop me from doing the one thing that I love: making music. If my melodies find their way into your heart, then there is still hope for me. If I can't prove that I exist, I can at least prove that my love for each and every one of you exists. Please, listen to my story, my symphony, for it is me."

Cover pic by Spotlight: askspotlight.tumblr.com