It is the year 3070, and Mankind is once again at war. The battlefields of the future are dominated by fierce, robotic war machines known as BattleMechs, and under their auspice empires have risen and fell. Now with the worlds of the Inner Sphere once again facing the drums of war, two mercenary units have set off on their respective missions, their only tie a common ride upon the back of a JumpShip.

Yet when a cosmic accident causes a misjump, they find themselves thrown into a world that they cannot fathom: a world where magic is a force of nature, where mythical creatures live and thrive, and colorful ponies live protected under the aegis of their monarchs. New choices lie ahead, decisions must be made, and the inner character of Humankind will be put to the test when the question is asked: to conquer, or protect?

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It is the year 1023 after the ascension of Celestia and Luna to the dual thrones of Equestria, and Ponykind is at peace. With Luna cleansed and Discord sealed away even more thoroughly than before, all looks bright for the future of the colorful equines. With friendship and optimism, they face each day with hope and vigor.

Yet, when the heavens scream as a foreign object tears its way into their reality, the princesses and their subjects face a new threat that they cannot fathom: creatures and machines from a world of death and darkness, where magic is unheard of and the avarice of powerful men drive the engines of war to crush the innocent under their bootheels. Can they survive the coming of these coarse beings, and can they maintain the magic of friendship in the face of Man's Inhumanity?

With Russian Translation provided by Undermind.

A crossover with the Battletech universe, though this is an alternate BT timeline of my own devising. [WARNING: Fandom related material and fanboy rant to follow. Non-Battletech fans won't care, read at your own risk.]

Because **** the Word of Blake and their munch-tastic "armies from thin air" BS. Yes, I know the Clans were almost as bad, but at least they had some sort of justification in-universe. Wobbies? No. Just no. I don't care that it was 15 years, you don't go from "fringe group of mutually-antagonistic and argumentative sub-groups following various degrees of religious mania" to "WE ARE THE SPACE NAZIS ALL WILL BOW BEFORE US" like that.

So for BT fans, this is a 'verse where the Second Star League is still around, the Wobbies still had their temper tantrum though it was smaller and more in line with a bunch of religious fanatics. No stupid "knock everything down for ClickyTech" Wizkids/Fanpro approach, nor any "hey let's shove a bunch of cheesy Level 3 stuff at the players to make the game even more complicated" Catalyst Games stuff. This is just good ol' fashioned 'Mechs wailing on each other, only with ponies. Who will also be wailing on 'Mechs. GLORIOUS.

Cover image by Icaron of DeviantArt.

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

Some things in this world happen by chance. Others do not. Twilight Sparkle is about to learn a disturbing truth that will turn her world upside down.

- Originally written May 2011 for Deviant Art

Reading this story first is strongly recommended:
(Blood is Thicker) http://ciroton.deviantart.com/gallery/26378692#/d3e1ndq

Credits:
~Image by JohnJoseco~ ~Edited by BrotherPrickle on Deviant Art~

Princess Luna, Mistress of the Moon, co-ruler of Equestria, is utterly bored, and tired of dealing with the bureaucracy. When she happens upon an uncompleted spell that promises access to other worlds, she finds a project that engages her as seldom before. Yet, some worlds are not so pleasant and safe as Equestria, and Luna is about to find out how denizens of one of the more dangerous realms entertain themselves as she is thrust into a bloodsport like no other.

The Tournament awaits.

A crossover with Unreal Tournament, specifically UT2k4, which I've come to regard as my personal favorite of the series.
There is some gore, but nothing worse than your usual FPS game made in the last 10 years or so. Rated Teen for that, and some foul language. (Because it wouldn't be UT without the smacktalk.)

Consider this as the soundtrack. Because that's exactly what it is.for Deck 17. So, freakin' EPIC.

Cover art commissioned from Atryl, who is a demigod of Art. Seriously, he's awesome. Go throw money at him.

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

The story of the newly promoted Admiral Twilight Sparkle, and her first command. A fusion fic with various science fiction series by David Weber, principally but not only the Honor Harrington books.
Cover image from Kampzvono on Deviantart, used with permission.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony