We all know the story of how the Princess’ young student and five friends defeated Nightmare Moon and brought Princess Luna back to our lands. But what if the tale were false? What if the young Twilight Sparkle on the event of her entrance exam had not been rescued by Princess Celestia, but instead lost her mind among the power of her youthful surge and had to be sent away, far away before she could destroy all of Canterlot with her newfound power. Now the feral unicorn prowling the Everfree Forest only vaguely remembers her past, slipping away from constant terrifying attempts to capture her.

And she is beginning to remember what true power felt like.

Editors include: Peter, Justin, Featherprop, Mitch H, and Bad Horse
Featured on Equestria Daily
Reviewed by Chris on One Man's Pony Ramblings and by Paul Asaran on his review blog
Now with a TV Tropes page

Physical books are available on Lulu.com
Monster in the Twilight (Paperback) 272 pages
Monster in the Twilight (Hardback)

Edit: Now a collaborative effort with Loyal2Luna

Commander Shepard has been through a lot, but now that the Reaper War's over he can finally relax and take a little R&R, right? Soak up the sun, grab a few drinks, spend some quality time with Tali, introduce a new race to the galaxy... wait, what?

In the aftermath of the war, a new species has been discovered amidst the destruction and fire. A species that have access to powers never seen before, powers which could prove vital to the continuation of galactic survival.

The Citadel Council has elected to send Shepard, along with the rest of the crew of the Normandy, to introduce Equestria to the universe outside of their solar system.

Now Shepard must wade through obstructive bureaucrats, antagonistic journalists, and the odd, angry prince in order to bring Equestria into a new age of space and adventure.

So settle in, it's going to be one hell of a vacation!

Now has it's own TvTropes page

An undead Emperor in need of a new body. A Spartan lost in space. A ragtag team on a suicide mission. What do they all have in common? They all wind up on the magical world of Equestria, where war has been forgotten. That, however, is soon about to change.
When each of them is about to be retrieved, ancient evils arise to unleash hell upon the unsuspecting world. When the forces of three galaxies clash around them, can our favorite ponies hold out against the onslaught?
This is a crossover involving Warhammer 40k, Halo, Mass Effect and MLP, and is also my first fanfic. Comments and reviews are welcome.
Rated T for language, violence, and general adult situations.
Now on Tv Tropes!

In 2185, during his campaign against the Collectors, Commander Shepard discovered a previously unknown species whose origins predated any other race in the modern galaxy. Following a daring rescue from their ancient sanctuary, the Equestrian Herd was brought back into the galaxy where, for the first time in eons, they must walk their own path.

Knowing full well the terrible threat that lingers on the edge of the galaxy, the leader of this newly freed race fights to secure her people’s future while attempting to prepare for the storm on the horizon.

This is her story.
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The long awaited Sequel to Mass Effect 2: The Equestrian Equation This is a reader directed story. Your choices will shape events.
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Also, this series has its own TVTropes page now! (Special thanks to user CrowMagnon for setting it up).

Brought to you by Loyal2Luna, this new Downloadable Content for Mass Effect 2 brings the fight to Equestria.

Just about ready to embark on their mission to stop the Collectors from further abducting human colonies, Commander Shepard and the crew of the Normandy SR-2 are given a new priority, when the Illusive Man tasks them with investigating the mysterious disappearance of a Cerberus science team.

Soon, what begins as a simple search-and-rescue unveils a mystery millions of years in the making, and the Commander finds himself thrust into a situation he couldn't possibly have prepared himself for.

Join the Hero of the Citadel as he uncovers the secrets, combats the demons, and ultimately decides the fate of the impossible world known as "Equestria."

For almost a thousand years, the immortal Nightmare Moon has reigned over Equestria as Empress. To the average pony, Nightmare Moon is an overarching enigma whose rule is absolute and whose wrath is terrible. But to Twilight Sparkle, who as an orphan has never known her parents, the Empress is something else entirely. When the young unicorn is brought under the royal wing as an apprentice, she learns a great deal more about the supposed tyrant than she ever knew. But as Twilight is introduced to life with her new mentor, she is thrust into a world of political intrigue, conspiracies and secrets. Secrets that were never meant to be revealed. As allies and enemies plot against the very peace of the nation, will Twilight fall prey to the perils of her new position? Or will she prosper and find in Nightmare Moon the mother she never had?

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My eternal gratitude to my editor, LordOfTheWrongs, without whom Night's Favoured Child would not be the story it is today.

Now with added TVtropes!