After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

This is the first book of The Humanity Within Trilogy. Its sequel is What I've Done.

I wasn't always like this, a monster, running through the woods on an alien planet. I was once a man. I had dreams, a girlfriend, and a great job.
Then They came. In the middle of the night, They scooped me from my home, and... changed me.

Now I'm a beast, a demon the like of which the world I've become stranded on has never seen before, scraping by on the fringes of society, hiding from the natives, and doing my best to avoid notice.

After all, who could ever be friends with a monster?

Cover Image done by the very talented PaintSplotch! You can find his FimFic account here.
And here is his DeviantArt Account!
Now 100% approved by Twilight's Library!
Mad props to my prereaders:
ThatPonyWithASword.
Admiral Applejack.
JXWheeler

When Twilight is accused of nepotism, her friends rush to her defense! Sortof.

Written in four hours during a speed-writing exercise. Totally unedited. Enjoy!

My name is Twilight Sparkle, and 350 years ago, Sweetie Belle and I vanished without a trace.
Now here we are, in the future.
Equestria has become a utopia, with everypony living in peace and harmony.
Everything is perfect. All a pony could ever want, and more.
My name is Twilight Sparkle, and I want to go home.

Editing provided by Stereo_Sub and JustAnotherTimeLord.

Cover art courtesy of Geomancing.

Reading by lieilengi

Spanish translation by Spaniard Kiwi

In a fit of pique, Twilight summons the Cutie Mark Inspector to Ponyville to conduct a cutie mark review of the townsfolk. When it transpires that every pony has been interpreting their cutie marks wrong, Ponyville is thrown into chaos. Has Twilight bitten off more than she can chew?

Shining Armor learns the most important tactical lesson of his life.

Audio version! https://youtu.be/YgDr0Xc6rN8

Now with a Spanish translation by Spaniard Kiwi!

It seemed like such a noble goal to Twilight: bring herbivores and carnivores together by finally destroying the ethical cost of meat.

She would be lauded by history as the greatest agent of harmony, not that it would matter to her. All that would matter to her is that she'd finally performed an act worthy of an Equestrian princess.

All it had to do was work.

HELLO, COMMANDER.

In response to the Equine threat, this council of nations has chosen to activate the XCOM project.

We have located the alien's homeworld, known as 'Equestria'. Your mission is to travel there and murder everything you see. Your team has the best weapons, armour and training. Literally nothing can go wrong.

Operation: Exploding Face is underway!

Remember, we will be watching.

Tirek won, and Equestria lies under his hoof. Luckily, some brave ponies remain that resist him.

Unfortunately, they're the Cutie Mark Crusaders. And they have a brilliant plan.

A companion piece to Bring Me the Heads of the Cutie Mark Crusaders! by CCC and Der Unter-gang by monokeras, tackling the same premise in a different way.

Cover art from the gallery of ROBBERGON.

"Dear Santa Hooves. My name is Apple Bloom, and I don't want presents for Hearth's Warming this year. I just want my cutie mark..."

Featured on Equestria Daily -- January 18th 2013
Fanfic reading by Scribbler
Reddit page
Download link for the 'FROM THE DESK OF TWILIGHT SPARKLE' paper