Strange nightmares are plaguing the ponies of Equestria.

Somepony must help ponies to face their deepest fears, but unless Princess Luna is able to discover who—or what—is responsible, the nightmares may never end.

Scootaloo is ready to prove that she can be as fearless as her big sister, Rainbow Dash, even if it means never having a peaceful night's sleep again.

It has been more than one hundred years since Celestia banished Nightmare Moon. While Equestria has enjoyed a century of relative peace and prosperity, there are still lingering tensions between the three pony tribes.

Shadow Kicker, a proud warrior of Pegasopolis, must navigate the treacherous noble court of Canterlot and address the concerns and wounded pride of her own tribe in a desperate effort to prevent matters from coming to open warfare.

Something has happened and Twilight finds herself in a strange and dark new world. The Bipeds here have strange magic, advanced technology, and a lot of problems. She needs a few friends, and they just might need her. WORM crossover. Deadpan29 has created some great supplementary material that is canon to the story.

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 Stardust

Times are changing for Equestria as Twilight’s return brings with it news of people and cultures from beyond the peaceful world everypony knows. Aid and volunteers are freely offered to help the besieged humans of Earth because every Equestrian knows that’s what good friends do. Unfortunately, making friends can also have the unintended consequence of making enemies.

When the monsters besieging the humans strike at Equestria with a level of brutality not seen in over a thousand years, the cry for help is sent to all the kingdoms of the world. Honored allies step forth to fulfill ancient treaties and oaths. Enemies, old and new, bury their grievances. An alliance never before seen in Equestria will be created to combat the monsters from the void.

And because of these events, a grim but welcome sibling to the XCOM project is born.

(XCOM/FiM Crossover)
(Sequel to Stardust, which I recommend reading before starting this. Fortitude Amicitia and Broken aren't required reading but are supplemental to the storyline)
(Gore tag for blood and violence)
(Alternate Universe tag because of the divergence from canon that Stardust has caused)
(Uses elements of Season 4)
(Coverart produced by the amazing Carnelian!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz and Setokaiva for prereading!)
(As of 03/07/2016, the prereading team consists of Arzoo, BradTheBrony, Noble Cause and Metallusionsismagic!)
(Complete with it's own TVTropes page as part of the Stardust continuity. Could use some updating!)
(Character tags will be added as chapters are added!)
(Featured 5/12/2014! Thanks folks!)
(Possible spoilers in the comments! BEWARE!)

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

This story is a sequel to You Can Fight Fate

Time loops? The end of existence as we know it? Fate itself conspiring against you? Who has the energy to deal with that kind of thing?

Not Cloud Kicker, that's for sure. She's a mare who knows what she wants out of life. An easy job, a nice house, and an endless supply of potential banging partners. Then one day a simple little flower vendor moves in down the street and everything starts to change.

As a side story to the main Time Loop Trilogy, you can expect massive spoilers in the comments for both the original stories and unwritten chapters of this one.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to MLA: Perihelion

It's been a handful of years since Twilight came into her own as a Princess of Equestria, a few years spent in peace and harmony without so much as an angry spirit or clandestine invasion to take away from the tranquility of Equestrian life. Unprecedented developments in the technological and thaumaturgical sciences seem to be preparation for something, though nopony realizes what that something might be.

Nopony except the Princesses, who have not failed to see the signs of impending disaster that began with the mass kidnappings just following the Summer Sun Celebration. When all their preparations are turned upside down, can an alliance with the mysterious Precursors turn the tides of the most devastating war in Equestrian history, while there is still anything left to save? Enemies and allies appear in the most unlikely of places, and friendship with a dying elder race can be more dangerous than an invasion of Dragons and Changelings. What is a pony willing to give in defense of harmony? What are they willing to sacrifice?

This story now has a companion piece, The Sunset Campaign! This story is designed to bring Harmony Defended more into line with the three-story version of My Little Apprentice. If you read Apogee and Perihelion, you may want to read that as well!

This story was written prior to season five, and as such any events which transpire therein may or may not be treated as canonical. All events up to and including "Twilight's Kingdom" are treated as having occurred, however.

A huge thanks to my Alpha Readers! Thanks to these wonderful people, new chapters aren't nearly so riddled with mistakes and errors as they used to be. Thanks to Sparktail, TwoBit, Withered Pyre, and Zutcha. Zutcha of course deserves double the love, since he's also the artist of the cover and any other fantastic art that finds its way into the story.

Being an immortal goddess and supreme ruler of a nation is stressful. But sometimes you just have to cope with weird things. These are short stories about things that might or might not have happened, but were certainly erased from Equestrian history.