"I have sworn upon the altar of God, eternal hostility against every form of tyranny over the mind of man."
-Thomas Jefferson

Three hundred years ago, Equestria tried to assimilate Earth.
They failed. They fled, rather than face justice.
We moved on. We conquered the stars, we made a civilization that spans across the infinite void. We built true harmony between species.
We thought we'd seen the last of Celestia, but as a desperate mobile colony on the fringes of known space came to discover, we were wrong.

It is time to finish what was started by our forefathers.

Based on TCB: Not Alone, by Starman Ghost.

EDIT: Following Starman Ghost's deleting of Not Alone, I've replaced the above link with one leading to a PDF file uploaded to mediafire.

EDIT (14/04/2014): The character of Evening Star was originally created by Starman Ghost. I am using her without his permission.

This story is a sequel to What if: Rarity from The Three Sisters met with Chrysalis

Choosing whether or not to visit Chrysalis has been bugging Rarity for a week since receiving an invitation to do so. But there seems to be trouble brewing in the Hive and Rarity now has little time to act. Either way, her family's future rests in her hooves.

Now with a TV Tropes page! Warning: Will Contain spoilers.

The world spins, years pass, and everything comes to an end. Except Celestia. She sits on the shore of the last ocean, watching and waiting for her own chance at death. Because everything comes to an end if you wait long enough, and Celestia is patient indeed.

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?

Stranded on a hostile, alien world, Twilight Sparkle and Rainbow Dash must depend on one another and a fellow alien castaway if they want to return home to Equestria.(originally published on FFN)

Driven by an intense Warp storm, a Rogue Trader vessel finds itself crippled and stranded above a world no human has ever visited. The natives are friendly; can the visitors say the same? A Warhammer 40k/Friendship is Magic crossover. Yes, really
(12/02 added epilogue to last chapter)

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.

An aspiring rationalist gets punted into Equestria - and instead of being turned into a cool griffon, or powerful dragon, or even a standard pony... discovers he is now a milk-cow, part of the herd.

Part of the Chess Game of the Gods crossover.

Set in the far future after Celestia and Luna mysteriously vanished and the sun and moon froze in the sky, Antipodes is the story of two ponies thrust out into the harsh new world on an adventure to uncover what happened to the world so long ago.

(I wrote this when I was 17. it's pretty rough in places, but i think the basic ideas i had here were pretty cool. it's got a good skeleton)

Spanish translation here: https://www.deviantart.com/spaniard-kiwi/art/Antipodas-1-3-953524835

Cancelled, but preserved for posterity.

Archer is not having a good day. He's recently been knocked unconscious and imprisoned by a Fae race, notorious for their animosity towards humans and each other. Instead of cannibalistic Merfolk or mischievous Fairies, he finds... talking ponies. Who want him to be their "friend."

He is sentenced to remain in a small town they call "Eqshana", until he can learn to "live in harmony" with its inhabitants. Unfortunately, a message from his king, Jove V, has turned his prison sentence into a mission of espionage. Now he must escape these no-doubt insidious creatures, and even more importantly, stay sane doing it. Along the way, he will answer one of the most important questions he has ever faced: Is there really nothing to eat around here besides hay?