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.

A minor injury leads Apple Bloom to learn that she and the other Crusaders aren't like normal ponies. Not having their marks has always been their common bond, but as the trio uncover their unique nature, it becomes clear that their lives are intertwined on a much deeper level. As they learn the secrets of their shared past, it leads to revelations about their friendship, families, and their long sought after talents. What they discover and accomplish along the way is beyond what anypony would have thought possible.

There is now a sequel! Three Wishes: The Hole In The Sun

And a (more or less) standalone Christmas Special set between this and the sequel. Cinder Claws: The Caribou Legend Of Kol-Klor

Big thanks to totallynotabrony, Dusk Watch, AugieDog, and Piquo Pie for prereading and editing help!

Scootaloo's life hasn't been the easiest. Being orphaned at a young age and brought up in the foster system came with its own set of challenges, not the least of which was a lack of older pegasi around to teach her how to fly. Fortunately, Rainbow Dash can help with that. With her honorary big sister taking a more active role in her life, Scootaloo learns much more about herself than just how to fly.

A story about love, family, and growing up.

Editing by Formerly Committed and Shellsh0cker.

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

==Originally written spring 2011== Equestria Daily Post==
GLaDOS is free of Chell, free to continue testing, when she discovers a portal gun Wheatley tried to repair with duct tape. When the portal gun catastrophically fails, the enrichment center, GLaDOS, and Chell are literally dropped in the middle of Equestria. The mute test subject soon finds the world of ponies far more welcoming than the human world. But GLaDOS sees possibilities. Let the testing begin... for science.

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.

There is a secret in Equestria. A secret the newly crowned Princess Twilight Sparkle doesn’t dare to believe. Like puppeteers pulling on marionettes, they have influenced Equestria for better and worse since the fall of Discord. So far they have been benevolent, but their potential for evil is vast. What’s worse, she doesn’t know their name. She doesn’t know their mission. All she knows for certain is one thing.

That they all seem to be zebra.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?