While she's providing veterinary care at the park, Fluttershy runs afoul with one of the more domesticated critters.

...Fluttershy would never kick a puppy on purpose, would she?

Editing by Formerly Committed and Shellsh0cker.

Dramatic reading here!

When the Cutie Mark Crusaders dig up an ancient magical artifact, they unleash a spell on the town that allows everypony to see a "lie meter" floating above each other's heads. While attempting to solve the mystery, Twilight Sparkle has to analyze the tenuous balance between friendship and honesty. She doesn't like what she finds.

Based on a story idea conceived by theworstwriter
Written and posted with his permission

Discord is a new draconequus now, and sworn to use his powers only for good, but that doesn't mean he can't still have some chaotic fun while on the job. Tasked with helping to reform a pair of thieves hiding out in an abandoned apartment building, the Spirit of Chaos decides to make a game of it. Two lost souls find their lives on the line as they gamble their freedom in a battle of wits against a grand master, in his own House of Chaos.

Part of the Borderworld.

The royal court of Canterlot welcomes its newest member with open forelegs: the human philosopher Voltaire, from Earth.

On Earth, Voltaire is known as the greatest enemy of tyranny in the history of literature, and a legend in his own mind.

On Equestria, the court betting pool is giving him a week before the Princess banishes him to the Moon.

Note: This story doesn't have sequels per se, but there are a couple of short follow-ups set in the present day ("Parade Coverage" and "Secret Histories"), and a prequel of sorts in "At the Inn of the Prancing Pony".

TV Tropes page.

Luna has had enough of Celestia's games, and has found the perfect means of revenge. Using a long-forbidden spell, she transforms her sister into little more than a small filly, all so she could pull the greatest prank ever. Unfortunately, she soon learns that before you fool around with dangerous magic, you really need to read the fine print...

A sequel can be found here.

Not so long ago, Equestria barely defeated two almost unstoppable creatures known as humans, which they called the Second and the First. Almost five years later, another one has shown up. The military takes up arms, the princesses are stricken with fear, and the Elements of Harmony assemble, ready for battle. But 'the Third' has no idea what's going on, and only wants to know how he came to be here, and how to get back home. Good questions indeed...But will he ever get his answers? Or will his predecessors' legacy catch up to him first?

“Side story/prequel to Human by DannyJ, but can be read on its own. Contains spoilers.”

In Equestria's far future, one thousand and five years after the return, a dysfunctional group of argumentative ponies must quest to defeat the most dangerous enemy of Equestria to ever live; the malevolent Lord Second, one of the only known members of the race of elder gods known as the humans, and the ancient cult who worships him, the Brotherhood of Man.

An over-the-top surrealist comedy, with slight serious elements. Expect a steady decline into insanity.

Cancelled, due to reasons of severe cranial trauma

Now with audio reading and prequel story, Shades of Grey, by Draven Eclipse.

Set in the far future after Celestia and Luna mysteriously vanished and the sun and moon froze in the sky, Antipodes is the story of two ponies thrust out into the harsh new world on an adventure to uncover what happened to the world so long ago.

(I wrote this when I was 17. it's pretty rough in places, but i think the basic ideas i had here were pretty cool. it's got a good skeleton)

Spanish translation here: https://www.deviantart.com/spaniard-kiwi/art/Antipodas-1-3-953524835

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

When Twilight Sparkle hits a wall in her research on Princess Celestia, a new face in Ponyville gives her the spark she needs to overcome it. But after his arrival, ominous events are set into motion. Soon, Twilight must choose her side in a conflict that will decide Equestria's fate.

As seen on Equestria Daily.

Google Docs Version.

Edited by Horse Voice.