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

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

You know that fan-fiction you typed last week? It's a part of the multiverse. So is the main canon of the show, as well as every single variation of the Equestria we know and love.

In the endless worlds of the multiverse, every possible alternate Equestria is explored.
And every single one of those worlds is in mortal peril.
That's where the Order of Destiny comes in.

It occurred one peaceful night. Half of Equestria awoke to the sound like a double-shot thunderclap. A percussion heard in the skies and rattling windows from Apploosa, to Canterlot, to Ponyville. Nopony knew what it was or what it heralded for the world as it drew a line across the nation.

For Twilight Sparkle, this isolated incident might have faded from memory after a time, if not for the strange rumors of a creature sitting on the hill on the outskirts of town.

These are her thoughts given written form. These are Sparkle's Notes.

Report EVERYTHING to the Princess.

The Cutie Mark Crusaders have always lived in the now, getting what they think needs to be done as a soon as possible, executing their plans just so they can move on to the next one right away, not thinking about the consequences till they’re right there in their faces. But when an attempt to earn their cutie marks goes too far, Sweetie Belle and her friends must face a horrible reality that sends their world into darkness and fear. How will the truth be uncovered and what will be sacrificed to undo this nightmare?

Hope is the faith of the young. Losing everything she holds dear, Puppysmiles embarks on the adventure of her life to find her mother, her hopes of meeting her again driving her through the horrors of a world not of her making. Too bad the Wastelands doesn't care about hope.

Eighty years after the events of The Dread Chitin, Equestria is a radically different place. The arcane science of the late Duran Thirk and the information found on the Star League library core have combined to catapult the nation's science ahead by hundreds of years.

Now, facing the possible aggression of a completely unknown alien power, Twilight Sparkle and her friends have to gather together once more, leading a crew of the best ponies they could assemble in a voyage outside their own star system. They seek to learn about their potential foe, to explore the galaxy around them, and possibly find allies and friends to stand alongside them. Who knows what they will actually find?

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.

After the Pandorica falls into the exploding TARDIS, it throws The Doctor through the very last crack in time, a crack through which he can cross universes.No TARDIS, no screwdriver, a whole new pony body and a certain unhappy plasmavore that fell through with him, The Doctor begins to think that perhaps his plan was not as fool proof as it could have been.

How will The Doctor protect the highly confusing, sentient ponies from the plasmavore that seems to be harbouring an unholy grudge against all things Timelord? How will he adjust to his new body? And most importantly, why does he have a sudden craving for...pears.

Well, at least he still has his bow tie.

This story is a sequel to Of Solicitude

Ten years after a massive war, Equestria has changed. The Empire now rules over all, giving peace and prosperity to those that deserve it, but some are against this new rulership.
The CMC, a small, raggedy group of smugglers working for the Apple family, are caught red-hoofed by an Imperial patrol. As the friends fight for their lives, they learn about themselves, each other, and the world they now reside in.
Meanwhile, in Canterlot, Emperor Blueblood has amassed a massive fleet and is preparing to smash what is left of the rebellion under the oppressive hoof of his Empire.

Fantart:

http://www.youtube.com/watch?v=cSqZZHhQa_I

http://www.youtube.com/watch?v=JE7m2dk8FB4&list=UUS5YHp6kB61DHIXt8THr4iQ&index=1&feature=plcp