Mis-communication has started many a war, but in this case maybe calling it a war was too generous.

The "war" is over, Twilight has successfully orchestrated a bloodless end to the Griffons' aggression, but only now does she realize that there is more to winning than she had first assumed, especially against a nation that holds war as a central part of their culture...

Now Twilight must deal with the aftermath while facing a challenge she never anticipated: being seen as a conqueror.

This can be read alone, but I recommend reading the letter that started it all for a chuckle and a little exposition. This series of expositional one-shots can also give some additional world-building.

Once upon a time, there was a pony. Her name was Celestia, and her purpose was to initiate a series of events which would ultimately result in in the production, encouragement, and maintenance of harmony in the world. This series of events started with eating grass.

Written during a speed-writing exercise at three in the morning. Experimental, pretentious, and totally unedited. Enjoy!

A strange mare arrives in Twilight’s library, claiming to be her future self—here to stop a terrible plague. But Twilight worries that this stranger’s bold claims may hide something more sinister.

Cover art by Cold in Gardez.

Dust has lived on the edge of Ponyville all her life, keeping to herself and studying. She knows Princess Twilight, and so when she realizes she's made a big discovery, she's eager to run to the castle and tell everypony the good news. But when she goes into Ponyville, they don't seem very happy to see her.

Why would that be? She didn't do anything wrong.

Twilight does some research into her tried and true teleportation spell.

Charity Beller has a simple life, but a good one. The little Amish community she's a part of provides everything she could ever need, if not everything she might want. But when a mysterious pink robot appears, damaged but full of stories about somewhere called 'Equestria,' she'll be tempted by a whole new world she never suspected existed.

The Hive serves the Swarm. The Swarm serves the Queen. The Queen serves the Hive.
***
Chrysalis is dead. Deposed. So is the way of the Changelings. But now the Swarm comes to a point of contention: none of their kind removed her.

The new Queen must be... selected.

They ask the Hive for a choice. But the Hive chooses not. No, the Hive has something else in mind, someone else who should choose. And so do two cultures, utterly alien to each other, find themselves in a dangerous dance...

After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

Eleven centuries ago, Prince Crimson Quartz grows up amidst the relics of past glories. The Crystal Empire, once the mightiest Power in North Amareica, now stagnates beside the rising Realm of Equestria to the south. A brilliant young stallion, Prince Crimson wants to avert this fate. Despised by his decadent family and unlikely to ever take the throne, the young scholar-prince searches ancient tomes and forgotten places for the power to restore the Crystal Empire to its ancient greatness.

Will he find his realm's salvation, or instead call up horrors from the darkest depths of spacetime? Can his friend, Princess Luna of Equestria, turn him from a ruinous course, or will she too be tainted by the touch of the Shadows?

(image by the talented NemoSpecific)

Y.O.H. 1515

As the Great Changeling War approaches its end, and the High Queen Nightmare Hunger is reduced to an ever-shrinking territory and number of Hives, the disgraced Theoretical Infiltrator Compound, already demoted to Logistical Aide, is no longer needed. The resource flow between Hives has ceased, and all she is now is a warm body noling particularly likes.

She is reassigned to to Hive Hunger's Provisional Hive Defense Swarm, a last-ditch unit of Warrior cadets and confused Workers having weapons shoved into their claws and being flung in the path of the Equestrian advance. She has read enough of the reports to know what this means.

Her life is over.

But now, after three long lonely years, among members of a Caste she would normally consider far beneath her, can the impossible happen? On the brink of her death, can Compound rediscover the sense of belonging that alone gives meaning to the life of a Changeling?

Can a pariah finally find friends?

ADDENDUM: AU after S6 finale.