(This story is sci-fi, and somewhat different to regular FIM stories.)
Aneki's world was small. It was spherical, and it only took a day to gallop from one side to the other. She had been taught nothing existed outside the sphere, but she wasn't so sure about that. Perhaps her world was a bottle, a container in which ponies had fled to live. A time would come when she gained the opportunity to investigate these things first hoof, if she lived that long.

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

Seeking her destiny, Flurry Heart has set off on a voyage through space... yet memories are not so easily left behind.

Written for the Imposing Sovereigns contest.

Special thanks to KingMoriarty, Fahrenheit, and Wing for editing.

The sequel to Wayward Courier. Read that first, or you'll get lost.

Two months after his first visit to Equestria, Thomas has returned. And this time, he's not alone!
Now the ponies have to deal with not only him, but a depressed snarky ex-Scribe and a Brotherhood Ghoul with her own list of incredible achievements and emotional baggage.
However, things aren't well in Equestria, as they quickly find out...

All major details relating to Season 3 are non-canon to this fic.

Spartans never die, they're just missing in action. This has never been more true for Jorge-052 as, after activating the slipspace drive that was supposed to kill him, he is instead flung into a strange world where war is but a distant memory. Will the aging soldier be able to adapt to this new peaceful planet? Or will his only salvation be found in finding a way back to his own chaotic universe?

(It's my first time, so be gentle)
Now featuring a TVTropes page by Sabo88

Disillusioned by the tragic events on Panchaea, Adam Jensen chooses to subsequently end everything and hope that mankind will find a solution to the augmentation debate by itself. Instead of welcoming death however, he finds himself in a strange utopian world filled with pastel-colored ponies.

Unfortunately, this does not mean Adam is allowed any reprieve from morally challenging decisions.

A/N: Deus Ex: Equestria is written in a way that does not confuse people new to the lore too much but feels familiar with the players. This story will feature a vote at the end of several chapters that will affect the direction of the story based on Adam Jensen's actions in the world. It is divided into three categories: Combat, Stealth, and Diplomacy. Choose wisely, for it will have long-standing consequences.

4131 EC, a year of no importance. Thousands of years ago, the entirety of our universe consisted of a single planet, an idyllic world of harmony and peace. Now, the galaxy is a hard place. The Age of Harmony is over, the old order is dead, and all that’s left of our once glorious civilization are fractured states in decline.

My name is Horizon Seldat. I grew up on a slum colony orbiting Luna six. My life just got a little complicated.

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

Applejack finds a strange visitor in her apple orchard one day, with even stranger stories to tell...
MLP/L4D2 crossover. My first story on FiMfiction.net! May add more tags as story progresses.
Credit for the image goes to brokencreation on DeviantArt.

I do not know where I am. Wherever it is, it's dark. Very dark. The only thing I remember is my name, and what I did to end up where I am now. The ship we boarded... it was so eerie. Everything about it. The distress signal. The empty corridors. The soundless hallways. And then there was the aliens; I remember them the most.