Chrysalis has heard rumors of a crystal mirror having the power to take ponies to other worlds, where they gain powers that put them on par with the likes of Princess Celestia or even the Spirit of Disharmony himself. She wishes to use the mirror for her own ends, so she can gain the power to finally have her revenge on the ponies that have taken everything from her and maybe regain her empire in the process. The world she finds, however, is the dark interior of a ship that is being overrun by dead creatures that will stop at nothing to kill her and the repair crew that came to fix the ship.

She must quickly get used to her new body while fighting the hordes of the dead, come to terms with all of the horrible decisions she has made over the years, and maybe see the light that the ponies talk about... provided that she, and her new companions, don't get killed first.

(Dead Space/ MLP Crossover)
(Part of the Universe 13 story series, though reading the other stories is not required)

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.

For all to long the false Empire Order has ruled over Inamorta, bringing naught but chaos in it’s wake. When Order causes this disorder, The Chaos Empire strikes. Now, Order fights a two front war as we rise up. We must unite if we are to take out Order! And tonight, we march!

For we are the Archidons, with bows so accurately piercing they shall fall before they get a chance to stand!

For we are the Swordwrath, swords so sharp limbs will sever at mere sight!

For we are the Speartons, born to die, but not before them!

For we are the Magikill, and today we summon Unity!

And we march, to take back our land, to push out the Chaos invaders, and to bring glory to our Empires!

Due to a rather unfortunate stroke of bad luck, a Blacklight Agent by the codename of "Deadman" has managed to get dumped into Equestria, with nothing to guide him but his training and what he learned in the field fighting The Order and SIVs in this new land.

Can he accept that this land is not in need of a remorseless killing machine like home was? Can the ponies accept a warrior soaked in the blood of nations as a person, and not just another monster in their land of black and white?

Perhaps only time will tell.

Knowledge of the universe is not required, and the story is currently undergoing editing in some of the chapters to correct my past mistakes.

Long ago, the Seraphim granted power to the Doom Slayer that he might conquer the forces of Hell. The Doom Slayer has won, Hell lies defeated, and now he returns to the Seraphim's holy realm. His mission is not over though, he has promises to fulfill, rewards to collect, and as always, evil to defeat. Let those who would harm this sacred land tremble, for the Guardian of Equestria, has returned!

(This story now has two sequels: Legion and the novella Doom Slayer.)