Something is gathering around the bearers of the Elements of Harmony. Something dangerous. Something magical. There's only one pony with the knowledge, the skills, and the muffins needed to save Equestria as we know it.
A Friendship is Magic: the Gathering crossover, taking place between seasons 1 and 2. Here there be flashbacks, briefly seen OC's, and possibly every emotion known to man or tiny horse. Abandon all pretenses of not being a nerd, ye who enter here.

Now with an amazing YouTube reading by the equally amazing AShadowOfCygnus!

During its two year search for Shepard, the lone Geth traveled across the galaxy, exploring worlds both known and unknown. After a blind FTL jump to escape from an Alliance patrol, it found itself in a previously undiscovered system, a system without a mass relay and completely cut off from the rest of the galaxy. It touched down on one of the worlds, a garden-like planet, with the intention of gathering data on any flora and fauna that may have been present.

Instead, it made a remarkable discovery.

Edit at 8:10 AM on 8/17/2014: Scanning...Featured Box Achieved! This unit humbly thanks all organics and fellow synthetics for their support!

A big thanks to my bloody brilliant proofreader AShadowOfCygnus. Don't stop being classy, buddy.
NOTE: This story takes place years before the Return, back when Twilight was just a filly.
Disclaimer: I own nothing.
My Little Pony: Friendship is Magic belongs to Hasbro.
Mass Effect belongs to BioWare and Electronic Arts.

(A Persona Crossover, accessible to those who have not played the games)

There is a problem plaguing Ponyville. For countless fillies and colts, every single night is filled with visions of their greatest fears, and it always seems to be at the same time: just after midnight. There are even rumors of a dark world where Ponyville is shrouded in an impenetrable darkness, and everything is still, as if time itself has stopped. While parents brush it off as part of their childrens' nightmares, the real nightmare for Ponyville is about to begin...

Cornerstone, a new resident of Ponyville, would prefer to simply continue his work building and designing homes, rather than dwell on these rumors. Unfortunately, when a pair of murders rock the town, he and a certain six mares and dragon assistant all find themselves drawn into the mystery of this other world. Thus begins the race to find its origins, as well as the murderer using it for their own nefarious purposes. And it all starts with a single question:

"Just who are you?"

"Why, you're me... and I'm you."

Cover Art by the amazing Acceleron

Zecora invites Pinkie Pie and Rarity to her home to share some zebra delicacies. Little do they know how familiar they are with these particular treats.

!Warning! This Contains: Micro, Vore, Implied Hard Vore

My name is Twilight Sprinkle, and my passion is donuts—from the delicate morsels I serve at elegant cocktail parties to the hearty pastries enjoyed by hard-working ponies who get up early. I don’t have friends, I don’t have books, and I sure as the sun don’t have any wings. I don’t care whether you’re here for revenge, for romance, or for a favor. My name is Twilight Sprinkle and I’m not who you think I am, so either buy a donut or get the hay out of my store!

(Edited by the mysterious the masked ferret.)

An older, wiser Trixie Lulamoon just so happens to have a somewhat above average student named Sumac Apple, whom she takes to meet with Twilight Sparkle, as Twilight is holding a contest, looking for the best and brightest students.

Sumac Apple just so happens to have a Horrendous Hypothesis that will not only change the lives of himself and Trixie, but holds an ominous warning for all of Equestria.

An entry in the Weedverse.

This story is a sequel to The Dresden Fillies: False Masks

It's been a while since the girls have seen their good friend Harry Dresden. Discord escaped, Luna attended her first Nightmare Night, the Royal Wedding was crashed by hordes of changelings, and Pinkie Pie threw a statistically improbable number of parties. They tried inviting Dresden, but between his new job and new apprentice, he always claimed to be too busy. The solution was obvious; if he couldn't come to his friends, they needed to go visit him. Besides, they say Earth is lovely this time of year. What could go wrong?

Rainbow Dash is gone.
Two Years ago she performed a trick to eclipse all others, and vanished without a trace. Everypony has started to get over it, although for five ponies the loss is to great even now. In respect the Wonderbolts do a performance for her at the site of her death. However, a certain Cyan mare is hard to kill, and is loyal to the ends of the universe, she can say that with certainty now, she’s been, and now she’s back. But what is she wearing, and where did she go for two years? Buckle up, for in Equestria there may be peace, but in the 41st Millennium, there is only war.

Now with a sequel: The Descent into Madness

Featured: 06/05/2014. Thanks so much to you guys.

Rated Teen for Violence and Grim dark references

This story is similar in ideas to Into the Black: A mares tale, Diamond of the Capital Wasteland and Halo: On the wings of Angels

New cover art done by Reapers Inc

WARNING: Comments contain spoilers. Proceed into that section at your own risk.

In the midst of Twilight's efforts to save the Crystal Empire from Sombra's return, she comes across an ancient artifact hidden away by the dark king. When she accidentally activates it, she brings two strange beings from an entirely different world to Equestria.

A Steven Universe crossover

Twilight Sparkle finds an ancient book in her library about teleportation magic. After an experiement gone wrong she and her friends find themselves in a strange land with new friends and make some new enemies.
She must now try to find a way back to Equestria or face the possibility of being eaten alive by a new threat that lurks in the skies above.

Copyrights go to their respective owners - Hasbro, Bethesda, etc.

Picture provided by DJMoonRay.

I am very biased in the real game so any changes such as sides of Stormcloaks or Imperials are already chosen and will not be changed.