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.

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

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Before her descent into madness and her rebellion as Nightmare Moon, Luna lived entire lifetimes as a mortal and traveller amongst the ponies of Equestria.

Restored to her true self, Luna knows she must return to her cyclic life to remain whole. As preparation she chooses to reacquaint herself with the lives of her subjects in this modern age, and in the guise of Sable Moonshine, unicorn scholar and distant friend of Twilight Sparkle, she travels to Ponyville to spend time with Twilight's companions. Despite the 'exciting' month of astronomical observation and scientific research planned by Twilight, Luna nevertheless finds time to work a day at Sweet Apple Acres. And then another.

And another.

Applejack, meanwhile, is pleasantly surprised by Sable's dedication and enthusiasm for hard work. She's less pleasantly surprised by Sable's enthusiasm for Applejack.

This story is a sequel to Ascend

Congratulations, Twilight. With Celestia and Luna on their constitutionally mandated vacation, you're in charge of Equestria. The position of Regent is an honored and hallowed one. But maybe it's a bit early to congratulate you. After all, whether it's a nobility jealous of your ascension, or a military unhappy with Celestia's decisions; one thing's certain: your reign will be anything but peaceful.

THIS STORY IS NO LONGER BEING WORKED ON. THE IDEA IS UP FOR GRABS; PLEASE CHECK MY USER PAGE FOR MORE INFORMATION.

Humanity has had the urge to learn and understand since the dawn of their species as Homo Sapiens. From the first telescopes and the study of the stars by sailors, to the colonization of new worlds, Human beings have pursued the unquenchable thirst for knowledge in all of its forms, no matter what the cost.

Now, in the year 4025, long after Humanity began expanding their reach into the deep expanse of space, a new world is found that defies all laws of physics and reality...

Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

I'm a spiteful old man. I've spent my entire life trying to fulfill my wish. The same thing every one of us wants.

The year is 2070. I'm the last brony alive, 82 years old. But I did it. I created the portal. And I'm jumping through. No regrets.

I've actually finished writing this story! Can you believe it? It's also available in book form, Click Here to go to lulu.com

In his search for someone dear to him, the Hero of Time is tricked by a fairy spirit and drawn to Equestria, where he soon finds that both realms share not only long lost connections, but also enemies both thought gone. With the alliance of Hyrule's greatest nemesis with the thousand-year-old menace of Equestria set on permanently ridding themselves of those who foiled their plans, it'll be up to the Elements and a boy to once again take on their roles as heroes and unearth a history few even know of.

Artwork:
Legend in the Making (CMC): http://fav.me/d5u6mgh
Olivia: http://fav.me/d5th7n2
They're after you (Poeny and AB): http://fav.me/d5moavt
Applebloom: http://fav.me/d5em3dv

MLPxLegend of Zelda crossover (if that wasn't obvious ahah)
Though not much prior knowledge of the Legend of Zelda series is required, you may not recognize some names if you're a stranger to the franchise. Takes place after Ocarina of Time, but before Majora's Mask.

(20-12-12) Chapter 1 has finally been rewritten!
Chapter 2 has also been corrected and updated!

Many years after sending her beloved protege to Ponyville, unease sits heavily on Princess Celestia's heart as her relationship with Twilight Sparkle seems to have cooled despite all they've accomplished together. On the advice of her sister, Celestia sets out to investigate and resolve the lost connection with her most faithful student. What does it mean to be a Faithful Student...or a Princess of the Sun?

Earned a six-star rating on Equestria Daily and featured on its very own TVTropes page!.

We all know the story of how the Princess’ young student and five friends defeated Nightmare Moon and brought Princess Luna back to our lands. But what if the tale were false? What if the young Twilight Sparkle on the event of her entrance exam had not been rescued by Princess Celestia, but instead lost her mind among the power of her youthful surge and had to be sent away, far away before she could destroy all of Canterlot with her newfound power. Now the feral unicorn prowling the Everfree Forest only vaguely remembers her past, slipping away from constant terrifying attempts to capture her.

And she is beginning to remember what true power felt like.

Editors include: Peter, Justin, Featherprop, Mitch H, and Bad Horse
Featured on Equestria Daily
Reviewed by Chris on One Man's Pony Ramblings and by Paul Asaran on his review blog
Now with a TV Tropes page

Physical books are available on Lulu.com
Monster in the Twilight (Paperback) 272 pages
Monster in the Twilight (Hardback)