After the events of “To Where and Back Again,” Fluttershy starts feeling bad for Queen Chrysalis, who is all alone with no other changelings and no love to satiate her hunger. So the pegasus finds Chrysalis in the Everfree Forest and offers to take care of her in the Sanctuary. Chrysalis reluctantly agrees, and finds that even though she doesn’t feel any love from Fluttershy, she feels fulfilled in other ways. The changeling queen goes through some inexplicable changes as she gets used to her new life, and wonders if it’s possible for her to love somepony else.

"Nopony exists but you, and you are but a thought."

Twilight's life as she knows it harbored a sense of security, but all that changes when Princess Celestia then arrives to deliver a message. To reveal the truth about Twilight's world that the mare's conscious mind has long since forgotten.

As her memories return, she is forced to come to terms with the fact that she was never Twilight Sparkle at all, but rather a structured thought experiment whose knowledge expanded through lives she herself requested to live in order to harbor a greater understanding of existence.

But sometimes there's one life among many that's the hardest to let go of...

Inspired in part by a "Three words" game in The Writer's Group, and Mark Twain's "The Mysterious Stranger".

Edited by Breath of Plagues

Featured on Equestria Daily!
TV Tropes page.

This story is a sequel to Changeling Space Program

The space race is over, and the third flight of ESA Amicitas is not yet even contemplated, but life goes on for the first changeling queen on the moon and her hive.

Faced with the necessity of keeping track of all her subjects and proving that they are, in fact, hers, Chrysalis decrees the Badlands Hive's first ever census. And normally this would produce merely normal levels of changeling stupidity, silliness and shenanigans...

... but what happens when a name pops up, and you can't prove that the changeling attached to it even exists?

Takes place in late winter after the end of Changeling Space Program and about two years before the beginning of The Maretian.

Written for FanOfMostEverything's Imposing Sovereigns IV contest, pairing Chrysalis and Unorthodoxy. (Group here.)

On one fateful day so long ago, six young ponies' destinies became inexplicably intertwined. Two in particular, however, discover a sense of being and of purpose that they couldn't have possibly foreseen.

Their days that follow are most certainly bright.

Our Days are Bright is a Rarishy fic featuring transgender self-discovery, and is told through a First Person perspective.

CW for mentions of body dysphoria, familial disputes, and pre-transition pronoun usage (young Fluttershy uses He/Him).

After many a thrilling adventure the Doctor drops the girls off in Ponyville to relax and recharge. But then Rarity's latest client, a diamond dog mining magnate by the name of Zeitgeist Stardust, shows up to announce that he'll have to cancel his order for a new ensemble for the Grand Galloping Gala... but as compensation, he's offering Rarity and her friends a trip to the fabulous Dragon Valley Resort!

There's no such thing as a free lunch, though, as there's trouble brewing in the mines beneath Dragon Mountain. A race of creatures known as "Grundels" are sowing disaster and trying to sabotage Stardust's operation, for fear that the digging will awaken an ancient evil. Are the Grundels' fears justified, and can the Doctor and his new companions put a stop to this?

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

What if Discord had not been turned to stone by the Mane 6? What if he had escaped?
It is three years later and the Mane 6 have moved on with their lives, all except Fluttershy, who cannot get the draconequus out of her mind. The others are happy in their new and comfortable lives, until their enemy returns and will only relieve Equestria of his havoc in exchange for a bride.

This has been adapted into an audio series.

Also, here's a dramatic reading by Pablo Didonna, and one by 666HellGirl1

Cover Art by Nstone53

French: http://www.deviantart.com/art/Une-Mariee-pour-Discord-La-fuite-440318295
Spanish: https://www.fanfiction.net/s/10203187/1/La-Novia-de-Discord

*Bronyland Pony Awards Nominee 2013

Come closer here—my heart, my host.
Come closer. Hear my heart, my host,

Is only staid with presence close.
Were love a potion, ample dose.

My night-ful bride, I need your boon.
My baleful bride, I need you soon:

For what’s eclipsed by half a moon?

[Cover art by by tractareSolidum
Now featured in the Royal Canterlot Library!]

After an unfortunate accident resulting in a mistimed prank, Fluttershy is left temporarily blinded, and Pinkie offers to take care of her. During an interview with a curious Twilight Sparkle, Fluttershy reveals an incident with an ancient temple leading the Mane Six to a dark adventure deep in the Everfree Forest.

Cover art by: Teknibaal [Link]

You can find a fantastic comic version of "A Sight for Really Sore Eyes," the first chapter. It was on DA by SpeccySY, but it can still be found here: [link]

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim