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.

If you liked this story, I've got a sequel going on! Take a look at Rescue at Midnight Station

Sometimes friendships, like ponies, are more than what they seem. Sometimes it's hard to tell what makes a friendship special. Sometimes, all it can be called is...Magic. When a Shuttle crashes outside of Ponyville, the friendships that grow from different beings from different cultures bring the ponies and humans together on common ground.

First off, the story idea....you know who came up with this brilliant idea...Kitsy-Chan.

Cover art by Alkarasu...

They say that Equestria was a paradise. I don’t know if that’s true, but I wanna believe it. There sure ain’t one in this piece of the ‘Verse. Maybe we coulda built one if it weren’t for the damned Confederation. Those bastards wanted every planet in the system under their hoof and wouldn’t take no for an answer. The outer planets fought ’em, and we lost.

It’s tough to get by these days with Confederation lawkeepers looking for an excuse to crack down, bandits and thieves crawling everywhere the Confederation’s not, and the Jesters prowling around the edges of civilized space. Honest work’s hard to come by, and honest folk are twice as rare. Still, a mare has to make a livin’ somehow. So that’s what I do.

Find a crew. Find a job. Keep flying.
– Rainbow Dash, Captain of Tranquility

Twilight and the other Elements of Harmony have saved the land of Equestria from Nightmare Moon, Discord, and the Changeling army, but now they face perhaps their biggest challenge yet. A challenge that lurks behind smiling faces and friendly eyes. A challenge that threatens to overtake the entirety of Equestria and enslave its inhabitants. But the ponies won’t face this threat alone. Help comes in the form of the most unlikely of companions: four teenagers, a hawk, and a blue centaur.

Coming back from a hectic job, the crew of Serenity experience a ship-wide malfunction as a bizarre incident occurs in space around them. Eventually all of the ship's systems clear and they think nothing of it, that is until they discover they've taken on a rather interesting hitchhiker.

An MLP/ Firefly crossover story, if that wasn't obvious.
I appreciate the story being shared around, commented on, liked, enjoyed, all that jazz.

Betazed, a lavish and beautiful world. Filled with singing waterfalls, lush fields, vibrant jungles, home to billions of people. All of that beauty, culture and history, and it could all come to an end.

Diplomacy is an endless game of chess. Faced with imminent destruction, the flagship of the federation has been summoned, but can this ship and its crew save the planet? Or will the home world of Deanna Troi be lost forever? With time running out, Picard may need to take chances, risks, and make a Knights Gambit.

Wow! Featured in four hours! Thank you soooo much!

I just saw that I forgot to give attribution to those who helped with this story, starting with Kitsy-Chan for helping the basic storyline and helping to make it into a 3 dimensional story, kalash for editing, and can't forget Hart's Fire, mocha, and so many others for input on this story as I started and continued it!

Art by Andrew Gavrilov

This story is a sequel to Where No Pony Has Gone Before

The Enterprise's mission to Equestria may be complete but perhaps it's not the whole story...

(This story and the preceding 'Where No Pony Has Gone Before have been bundled together on Space Battles Forum: https://forums.spacebattles.com/threads/where-no-pony-has-gone-before-star-trek-tos-my-little-pony-friendship-is-magic.620290/)

Just a normal day traveling through the 'verse on Serenity, then Mal finds that his ship has been invaded by talking technicolor ponies, and the crew didn't tell him until 10 minutes after.

After a natural cataclysm destroyed their homeworld and the Equestrian nation scattered to the stars in the evacuation, the Main Six and their immediate family in Ponyville drifted among the stars in an escape pod for weeks before they were found and adopted into the crew of the Federation Starship Voyager.

After two decades of tyranny, the end of the Galactic Empire had come to pass. The Emperor Sheev Palpatine, also Darth Sidious, the Dark Lord of the Sith, was slain by his own apprentice, Darth Vader, in attempt to save his son's life. His life-support system heavily damaged in the process by Darth Sidious's Force lightning, Darth Vader did not survive and died in the hands of his son, on the board of Deathstar.

Yet that was not the end.

What nobody knew was that the prophecy of the Chosen One has never been truly fulfilled and that the defeat of the Sith was merely the beginning of all glorious things the Chosen One had been destinated to do.

Through the arcane power of The Force, Vader found himself resurrected and revitalised on a strange world, with a second chance to redeem himself for all the atrocities he had commited. In time, he may bring forth things that would change the very course of the Galaxy. Only The Force will tell.

P.S.- Big thanks to mrkillwolf666 for all support he gave me. May the Force be with you!

P.P.S.- Special thanks to Bringiton6611 for editing. Teh Furce is strung wit dat one!