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.

Investigating primitive radio transmissions detected on a long-range Federation listening post, the Enterprise investigates a planet far in the unexplored border space of the Alpha Quadrant. There, they discover a primitive planet just starting its industrial revolution--a planet complete with extensive lunar colonization and in the process of launching its first warp-capable ship.

The failure of the alien ship initiates first contact--with a race of adorable talking horses. A first contact with some unique diplomatic idiosyncrasies--and hints of a more sinister plot behind the warp-vessel's destruction.

Every schoolfilly has heard of the Federation - the tall, mysterious, magicless beings from another world, who visit only rarely and briefly; waiting, they say, for 'stable planetary political unity'.

This is the story of when they first visited Equestria; of early contact between the Princesses and the Federation. It is also the tale of how Princess Luna, with some help from the House of Sparkle, managed the first fully Equestrian warp jump; and of how Spike became the first dragon in space.

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Additional note: There is an alternate ending for this story, which can be found over here. It follows on directly after the chapter titled Further Communications (and there is a note in the author's notes for that chapter to that effect, with another link).

The reasons for the split are contained in the comments to this story. (Note: Said reasons contain spoilers)

The Enterprise is sent to investigate a bunch of mysterious signals that ripple from deep within an unexplored area of the Gamma Quadrant. In their investigations, they come across a strange creature—a small white unicorn with an adventurous spirit. Lost in space, she just wants to go home, and the mysterious signals are her best lead.

However, unexplored space is always filled with strange new worlds, vast mysteries... and dangers the likes of which no one can be prepared for.

Part of the Transcendental Sequence. (The start, actually!)

"Secretly" a mega-crossover. No previous knowledge of any franchise should be required to read.

Edit: story has been canceled, alas.

Major Editors: Ebony Sable, Shilic, Code/GunGoose

Cover art: JumboDS64, my Krita skills, this, and this.

-GM, master of The Beginning

The USS Exeter, still damaged after a recent battle, scans a certain planet and finds evidence of much-needed dilithium crystals on the surface. Scans also show it's a pre-warp civilization, so the Prime Directive is in full force.

But they need those crystals, as the nearest starbase is hundreds of lightyears away. They only need a few pounds of them to repair their warp drive, then they can be back on course. How hard could it be to beam in, get the crystals from the primitives, and beam out?

What they don't know about is the white unicorn who's been using them for her dresses.

Those poor fools...

This story is a sequel to Harmony Among The Stars

The ES Harmony has returned home, Princess Twilight has been reunited with those she holds dear and everything has returned to complete normality.

Then there is the mirror portal to Canterlot High, which she and the senior staff of the Harmony had discussed at one point in their journey, filling the Princess' curiosity. It has been closed for around two millenia, so who knows what could be on the other side?

And then there is Discord. He seems to know something, and urges the Princess through.

All this, so the Princess can meet some very enterprising people. Discord has brought the popcorn.

(Featured on 12/12/2017)

Princess Twilight has seen some strange things in the past few years. She made the best friends a mare could have, she had some amazing adventures, became an alicorn princess, saved the world a few times, and got a palace to call her very own. Yet for all that, the strangest has yet to come.

There are new strangers in Ponyville. That's not too odd, but they're not ponies. They're human! But they're not like any human Twilight saw on the other side of the Mirror. Their magic isn't like anything she's ever seen, either. She'd love to learn more, but there's a problem. These humans could give Fluttershy lessons in keeping out of sight.

Dealing with snooping aliens was not exactly what Twilight had planned to put on top of her royal agenda.

I started writing this back before Season Five. It's not a new idea, not hardly, but no matter how many first contact stories I sifted through, always it was from the alien perspective. The pony perspective would come to the fore only rarely, and usually only with sizable external influences.

This story takes the idea of an alien observation team but is entirely from the locals' standpoint. What do you do when there's an alien science outpost next door?

Equestria finds itself caught in the cold war between the United Federation of Planets and the Klingon Empire. Can friendship prevail, or will this cold war turn hot, despite their best efforts?

This is a crossover with Star Trek, taking place in late 2269 of the Prime timeline, during the fourth year of the five-year mission of the original television series. It's not a crossover with the movies made by J.J. Abrams. It is mid-season five or so for Friendship is Magic. it is my humble offering for the fiftieth anniversary of Star Trek, which debuted September 8, 1966.

Thanks to FoalsHalf for being essentially my co-writer/sounding board, and to all those who have helped with proofreading and editing.

Space Battles thread.

Trope page... some day?

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/)

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

The One Small Trot, Equestria's first starship, prepares to leave Equus and break the warp barrier. The journey of a thousand light-years begins with this small step.

This is a crossover with Star Trek, and a sequel to Where No Pony Has Gone Before. I have written it in celebration and honor of the fiftieth anniversary of Apollo XI's touchdown in the Sea of Tranquility.