Equestria and the Crystal Empire have fallen to the Changeling Hegemony, led by the brutal Queen Chrysalis at the head of a mechanized horde of guns and tanks. Princess Cadance stayed in the Crystal Empire; Princess Twilight stayed in Equestria. Chrysalis rules the continent, only defied by Nova Griffonia, the poor Griffon colony in the north.

Across the ocean, the Griffonian Reich pledges to reclaim its lost territory, sundered by revolution a generation ago. While the Alicorn Sisters retreat to New Mareland, Princess Flurry Heart and Shining Armor turn to Aquileia, the Republic born out of the ashes of the Griffonian Reich. The Kaiser of the Reich is only a child, subject to a regent bent on war and conquest.

Flurry knows the Reich and Chrysalis have worked together.

She knows that war is coming to Aquileia.

She knows that Celestia and Luna abandoned her mother and Twilight Sparkle.

She knows that the world is on fire, and she is the last true Princess of Ponies.

She knows she will go home.

Cover Art by Opal Radiance, commissioned by Sunstreaker.
https://www.deviantart.com/opalradiance

Crossing Guard works in Equestria's Immigration Department: among other things, he serves as the final check on whether a non-pony can take up residence in Canterlot. It's not a simple job, especially given the follow-ups when a new resident or citizen-in-waiting inevitably gets into trouble. But Gerald Gristle is an exceptionally calm applicant, Crossing's tired from a long day, and so he allows the griffon to begin the five-year process, with the announced food supply business set to open two weeks in.

Which is when Crossing finds out just what kind of food the griffon is supplying.

After all, carnivores and omnivores have to eat too...

(Part of the Triptych Continuum, which has its own TVTropes page and FIMFiction group -- but can be read as a stand-alone, and no knowledge of the other stories is required. New members and trope edits are welcome.)

Now with author Patreon and Ko-Fi pages.

The Elements of Harmony. Six artifacts of legendary power that have provided for the peace of Equestria for over a thousand years. While Queen Chrysalis managed to deny the ponies their ultimate defense, she still lost to a different unexpected surprise in the form of a love-powered shield spell.

However, the Elements won't be so easily denied. Unbeknownst to anyone, they awaken in their vault and cast Chrysalis into another world to teach her a lesson or six about life and harmony.

Stripped of her power, trapped in a form unfamiliar even to a changeling, and at the mercy of the locals, Chrysalis must learn how to get along with others before she is allowed to return to save her hive. And if successful, she may just be allowed to keep her new friend... If he's willing, and if he can survive the drawbacks of being one of the rarest changeling classes ever seen:

A breeding drone.

Join a spoiled rotten queen and a workaholic electrical engineer in the retelling of an adventure that brought them together across the boundaries of space and time. Because sometimes, a little change isn't all that bad.

(Changeling Drone 'Gazer' design artwork courtesy of oFimFiction.net member 'More Dakka')

Twilight Sparkle, Celestia and Luna are transported into a strange alternate Equestria, the Land of Always Summer, where the day lasts forever and a terrible queen rules with an iron hoof.

Feel free to check out or add to the story's TV Tropes page.

Twilight Sparkle never was a Unicorn and she didn't even know it.
What happens when her true heritage comes to light? Will she willingly embrace it? Or will she be forced to?

Beware of spoilers in the comments!

Edited by uTTerAbsurdity, Zervziel, Stormwatch and Gwenio

Cover art by the talented Cartoonlion and colored by the equally talented Stormwatch, original can be found here

Click here for the Tvtropes page

Dreams are such delicate things, and Scootaloo’s are more fragile than most.

But in Equestria, dreams are protected. Sometimes a filly just needs a helping hoof to learn how to hope again.

Edited by Knight of Cerebus

Cover art by Joemasterpencil. Go check him out!

This story has a reading! Slightly older version of the story, but the reading is very well done. It can be found here.

Weevil and Echo are a married changeling couple who, amongst thousands of others at a time of mass migration, have left the Changeling Kingdom in search of a better life in Equestria, the so-called 'land of love, tolerance and opportunity'. Now Equestrian citizens and living in Six Points, a diverse and deprived district in Lower Manehattan, Weevil and Echo have opened their own business and are trying their best to raise their family and simply live their lives

Of course, raising a family is never easy wherever you live, especially in this bizarre urban jungle populated by friends, enemies, and all out crazies. But through it all, Weevil keeps a level head, an unwavering dedication to his friends and family and his values, and by doing so will come out on top out of whatever this Celestia-forsaken city throws at him.

Hopefully.

Edited by Chaodiurn and First_Down.

This story is a sequel to Guiding Light

By her mere existence, Princess "Derpy" De Raptura ushers in a new era in Equestria's history. The first commoner to ascend the throne, the first new monarch of Equestria for more than two thousand years, Derpy faces the unenviable task of bending a fractious and ambitious political establishment to her will when her experience amounts to little more than planning the best delivery route each day.

Yet it seems that Derpy must face the true price her new-found power demands. To raise the sun she must love the whole world, but to give that love she must endure a burden far greater than she could possibly imagine.

Book one of the De Raptura Chronicles

Ditzy "Derpy" Doo, once a humble mail mare, was elevated to godhood in a last, desperate act by Celestia moments before she and the entire royal family disappeared. Now the newly crowned Princess De Raptura must contend with the machinations of a court completely alien to her, reconcile with her daughter, make peace with Twilight Sparkle and learn how to control the sun.

And she's fairly sure she still has a package to deliver.

The story continues in To See The Light

Also available on Google Docs!

"This story differentiates itself from other 'bad things happen to Equestria' stories with its smart character work and realistic, powerful emotion. We need more stories like this." -Pre-reader who likes sky pirates

Short description borrowed stolen from FanOfMostEverything.

In the far reaches of Canterlot Castle, high above in the towers lived the archmage. Everypony knew her, yet few had met her.

Twilight Sparkle sighed, having teleported away another noble seeking favors before reaching the top of the stairs for the second time today. They never learned. As the archmage, she already dealt with political squabbles far too often without inviting them into her home. Aside from personal favors for Celestia, she did what was required of her position and then returned to seclusion and research.

The nobility grumbled that no archmage should be a commoner, and Twilight’s disrespect toward them proved it. Each and every time they were forced to bow to her, they hated what they saw: the position, the status, the deference.

Was she not powerful? Was she not great?

Twilight, now reading through dusty scrolls and long forgotten tales, wrote in her notes — notes gathering dust of their own. A brief thought flashed through her mind.

Am I not powerful? Am I not great?

And then Twilight picked up The Tale of the Royal Pony Sisters.

Defunct side stories told in Across the Boundary. They can still provide a little context, but when in doubt, the main story here is canon.

Cover art provided by Lafiir