Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

Cloudsdale. Bastion of the Pegasi, linchpin of weather control, home to the Wonderbolts. A magnificent metropolis gracing the skies of Equestria. So what happens when an oblivious human starts stumbling around in a sailplane? As they say, hilarity ensues.

The Caprica. At one time, an impressive piece of technology for humanity. Originally built for peace; retrofitted for war. But now, Marcus is all that remains of the human race after a hostile alien invasion, and he uses the only life he's ever known to escape his captors. Making a blind jump to unknown space, his skills as a pilot, and as a man in uniform, will be put to the test.

Rated teen for language and some adult situations.

The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

TV Tropes
https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2

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.