Princess Luna's Lunar Stallions kidnap Twilight Sparkle when they see how lonely Luna is, and give her to the Princess as a gift. Nightmare Moon emerges from Princess Luna's psyche during the sleepover. The dark goddess would love nothing more than to have the beautiful mare all to herself, and the resulting chaos forces Celestia to call a psychologist to sort out Luna's multiple personalities.

Princess Celestia will at last get a taste of Twilight Sparkle. No, not in that way! The whole Elemental Harmony Squad is involved... no, still not in that way!

Popsicles will be prominently involved... and again, not in a naughty way. The only naughty pony here is Luna.

Twilight Sparkle never was a Unicorn and she didn't even know it.
What happens when her true heritage comes to light? Will she willingly embrace it? Or will she be forced to?

Beware of spoilers in the comments!

Edited by uTTerAbsurdity, Zervziel, Stormwatch and Gwenio

Cover art by the talented Cartoonlion and colored by the equally talented Stormwatch, original can be found here

Click here for the Tvtropes page

Two thousand years after the return of Princess Luna, Equestria's technology and magic has advanced far enough that the once far off dream of faster than light travel is now a reality.

And that reality is the ES Harmony, the pride of its designer, Princess Twilight Sparkle, and Equestria's first FTL capable starship. It is due to make its maiden voyage to travel further than anypony before it.

And yet when they receive a distress call from origins unknown, this ship's maiden voyage will become one the crew will never forget.

(Featured on 31/7/2016)
(Not a strict crossover with Star Trek, but here Equestria Girls takes place in the Star Trek Universe)

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)

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.

Sergeant Stronghoof has been given the highest honor that a guard can hope for. Without being promoted to Captain of the Guard, that is. He has been given the assignment to be a bodyguard to Princess Cadence herself; during her wedding no less!

Now, technically he shouldn't listen in on her when she's getting ready for her wedding, but she's rumored to have a lovely singing voice. Once she begins singing, he overhears some interesting things.

Written because while This Day Aria is a spectacular song that I adore, I can't help but feel that her singing so loud would have attracted attention, especially when you consider that Twilight heard what the real Cadence was singing.

When the mane six go to see a Wonderbolt's show in Canterlot, Fluttershy decides to not go as crowds of that size make her too nervous. So, Princess Celestia decides to spend the day with her instead while her friends are away. The two decide to play a few simple games of chess to pass the time...

Find this story and more in a print copy! Just click these words here!

It took many long years and far more defeats than he'd care to admit, but at last—at long last—victory was finally within the great Ahuizotl's reach. Absolutely nothing, not even that meddlesome Daring Do, would be able to stand in his way any longer. Yet even with his arch nemesis facing her inevitable demise and the ultimate power literally in his grasp, he can't shake the feeling that he's forgotten about something.

One tiny, crucial detail. Something very important. As in, 'could easily ruin his plans if not attended to' important.

...

Eh, maybe he just left the oven on again.

A Diamond Dog king, feeling bold after gathering an army of 100,000 dogs, decides the best way to flex his new muscles would be to invade Equestria for past perceived slights. As such, he sends a letter to Princess Celestia with a declaration of war.

It goes about as well as you'd expect.