Friendship, the Final Frontier.
When a Starfleet ship discovers that the Orion Syndicate is enslaving ponies, her commander decides to do a good deed and return the rainbow-maned pegasus home to Equestria. Things don't go smoothly for the crew of the USS Judges, but what they find may be one of their biggest discoveries ever.
A Friendship Is Magic/Star Trek Online crossover.

====Originally Written June 2011=====EQD Link====
There is a shadow to all of existence, a place that all worlds are shielded from by a thin veil. A Dark Place, where a single presence plots and struggles to consume all creation with its darkness. The author Alan Wake is one who has defeated this Dark Presence, but to save his wife and his world Alan had to remain trapped in the darkness.

Now, through his struggles to return to his wife, Alan has unintentionally released the Darkness and an old villain upon Equestria. To fix the mistake, Alan starts a new story with Twilight Sparkle as the protagonist. Can the unicorn find the strength to face the darkness, or is all of Equestria doomed to be the victim in the dreadful horror story?

Note: Story assumes no preceding knowledge of the game Alan Wake. Written for any MLP:FiM fan to enjoy.

Following a near fatal incident involving her magic, Twilight goes into a deep coma. Her friends continuously visit her in the hospital in hopes of seeing her get better, but each day things worsen for the unicorn. Knowing that their dear friend may not recover, they begin to ponder upon their friendship and what they will do without her there. As time passes, they slowly begin to lose hope and slowly stop visiting their dear friend, who they fear is gone.

Meanwhile, Twilight finds herself in mysterious dark void, which constantly changes. Her mind is haunted by disembodied voices from her hospital room and by two mysterious ponies that she seems strange familiar with. Trying to find out where she is, she traverses the dark void in search of answers. But what she finds isn't what she expected... And it brings upon a terrible realization of where she is and how she got there.
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Cover art by jewlecho on DeviantArt.

Former "master thief" Sly Cooper had given up his old, criminal ways for good and settled into a new life with his love, Carmelita. But when an alien god of chaos spirits away and imprisons his lover and his friends, the last member of the Cooper Clan must take up his cane once again to get them back.

The deal is simple.

Come "willingly" to a peaceful, tranquil world populated by magical, colorful, talking ponies, and "acquire" six pieces of ceremonial jewelry in exchange for the release of his friends and the promise of a safe return to Earth. Piece of cake, right?

Right?

Sly Cooper and all related properties and art belongs to Sucker-punch Studios and Sony
MLP belongs to Hasbro & Lauren Faust
Cover art by the fantastic Foxinshadow
Proofreader, Editor and sometimes Co-writer: 2dextreem

*WARNING: Contains spoilers for all three Sly Cooper games in the first chapter. Takes place before the events of "Sly Cooper: Thieves in Time." In the MLP universe, this takes place between seasons 2 and 3, a couple of months after the finale of season 2.*

If you favorite, also like. Likes and comments pay the bills and make the chapters come more quickly.

This story is a sequel to Order from Chaos

Worker has found happiness, health, and most importantly, home. Now he struggles to defend those who made his new life possible while he wrestles with his own demons.
A belated sequel to Order from Chaos.
Concluded in Hope.

Comet takes his job too seriously. Angel doesn't take anything seriously.

Comet joined to protect kingdom and princess(es). Angel joined for adventure and danger.

Comet isn't interested in mares. Angel can't stop talking about stallions.

Comet is a pegasus. Angel is a bat pony.

Together, this unlikely duo goes through life as Royal Guards from basic training to fully fledged guardsponies. Who knows? Maybe they'll even start to get along.

Cover art by slawomiro.

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

Humanity has grown to control most of the Sol system, and looks to distant stars for further expansion options. When probes discover an uncannily-earthlike planet at a vast distance, the Solar Government takes on a project larger than any before it.

A colony ship, carrying over seven thousand people, the Eclipse is constructed. Thanks to its translight engine, it is capable of making the journey within two decades. The expedition is launched with high hopes, its crew made up of the best and brightest, setting out to prove that the vastness of space was no longer an insurmountable obstacle, that landing on distant worlds full of life was no longer just a pipe dream.

What happens when this colony ship's crew arrives at their destination would forever change humanity's outlook on the rest of the universe, as well as what could be deemed possible. Supernatural beings, energies unexplainable, and most importantly, sapient organisms all populate this mysterious, fertile world. In all of its extensive preparations, is the Eclipse versatile enough to tackle the task assigned to it? Or, more importantly, is its crew?

Featured on Equestria Daily 1/1/2013.

Pre-read by Stringtheory and Milo. Proofread by Erumpet and Demetrius. Thanks! Contains some hard and some soft sci-fi elements.

...The Continuum feels this species may be a real threat to the Q. However, they also show a unique ability to contain their power. They do not appear to use their abilities for power, greed, or war. We need to see if the species as a people are a threat to the Continuum and not just their abilities.”

“And locking me away in a statue, to rot away in a garden, doesn’t show that?” The face on the statue squirmed and struggled to free the rest of its body.

“No. It doesn’t,” said Q. “But it would seem an opportunity has presented itself. The Enterprise is heading for this region of space. Perhaps you could utilize their presence to…provoke…a situation?”

Both Q started grinning together. “Oh you know me too well, Q. I always enjoy seeing my favorite starship captain.”

The blond Q reanimated the rest of the statue. Discord stepped off the pedestal onto the soft grass. “This is going to be so much fun,” said Discord as his shape began to contort and transform. Within moments a familiar figure in a Starfleet uniform was standing where Discord had been a moment before. As the pair started walking away the blond Q said, “Just remember, Q. This isn’t just some random species to be toyed with. Any species RELATED to the Q, can KILL the Q!”...

(Season 2 Discord)

Never Seen Star Trek: The Next Generation? Here's a brief introduction to Q: http://www.youtube.com/watch?v=kBwoEXlTph0

Credit to Suddenly-Steinberg for the cover art:
http://suddenly-steinberg.deviantart.com/art/Discord-x-Q-312694442
MLP Season 2

The Medallion of Light and the Medallion of Shadow are some of the most powerful yet obscure artifacts of antiquity. Created by a now-vanished cult of assassins, the two devices together give their bearer the incredible power to walk the worlds with but a single step.

Nefarious forces are closing in on both artifacts, and very little stands in their way. Heinrich Himmler's agents covet the medallions for the greater glory of the Third Reich. Ahuizotl's simply want their master to get what's coming to him: the world, and everything in it.

With the fate of all good people and ponies in doubt, one thing's for certain: saving two worlds would be one hell of an adventure. And if adventure has a name, it must be Daring Do… or is that Indiana Jones?

Will our heroes win the day? Find out in... Daring Do and the Medallion of Shadow! Or, Indiana Jones and the Medallion of Light!

NOTE: there will be some violence in this story, but nothing more than you would expect to see in an Indiana Jones movie-- so I didn't check the "gore" content box.

Artwork by Tzelly-el.

Special thanks to SapphireStarlightPony & Rated Ponystar for helping with the brainstorming on this one.

Thanks to this stupid thing I've had the Indiana Jones theme song stuck in my head for like the past four days and I am about to claw my eyes out AAAAAAAHHHHH @_@