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 an unknown accident Twilight Sparkle and Rainbow Dash awake to find themselves sharing the same body! Now they must struggle to hold themselves together as their world is turned upside down. How long can two ponies exist in a single mind? It’s a race against time as they search for answers before it’s too late. When all is said and done, you’ll never look at Twilight Dash the same way again.

What would you do if you've gone where no mare has gone before, and have no idea how to get back?

Rainbow Dash found herself alone in a strange, magicless world governed by entirely different natural laws than Equestria, ruled by a race who thought themselves the only sentient species in the universe...

After many millennia of relative peace, the world of Equestria is suddenly plunged into a dark universe where there is only war. And its appearance has caught the attention of the great galactic powers. The future of ponykind hangs in the balance as they are forced to confront the horrors of a galaxy scarred by hatred, carnage, and the laughter of thirsting gods. Warhammer 40k/MLP:FiM crossover.

It's April Foal's Day and Applejack is, as usual, the recipient of many pranks, much to the amusement of her brother. When she enlists Twilight Sparkle to help with her revenge things get a little out of hoof.

After an accident, Twilight's life is turned upside down and changed forever.
With her friends standing by her, she must manage to overcome new obstacles, learn a new way of life, and discover just how long secrets last when hidden from those who know you best.

-----------------------------------------------------------------------------------------------------------------------------

Now in audiobook form!: Youtube

Welcome to Trotondo, where the lakes freeze overnight and the snow never stops falling.
Welcome to the outermost Equestrian colony, where the foreign threat is so marginally low that only two royal pegasi guards were needed to keep it safe.
Welcome to the town protected by Dawn Guard and Dust Mote, two peacekeepers so hopelessly in love that they don't even know it.
... Thankfully, the other four hundred and thirty eight denizens of Trotondo are more than willing to help resolve this predicament.

Part 1: Lyra's Pyro Predicament
Part 2: Twilight's Demoman Devastation
Part 3: King Sombra's Robotic Retaliation

After receiving a strange book from Pinkie known as "The Bombinomicon", Twilight wakes up one morning to find that the mystical tome has been stolen, by...Twilight?

Things quickly unravel as RED Team's Tavish DeGroot (Demoman) and Spy find themselves not only trying to get back home, but also fighting for their lives as villains from the Team Fortress 2 universe combine forces with some of the most dangerous foes Equestria's ever seen!

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

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!