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.

After attempting to impress the judges during her entrance exam for Celestia's School for Gifted Unicorns, something transpires that alters Twilight's life irrevocably, as well as the destiny of all Equestria. In a very literal manner, Twilight metamorphoses into the embodiment of magic, much akin to how Discord embodies chaos. How will this unprecedented transformation shape forthcoming events? And how will Twilight grapple with mastering the newfound god-like abilities that have been unexpectedly thrust upon her?

Have you ever seen a pony that just seemed out of place? Perhaps some mannerism, some behaviour that just struck you as odd? Some piece of clothing that didn't seem quite right? perhaps a coat or mane whose colour just seemed flat-out weird. A strange build, a strange voice, or maybe they were perfectly normal, except that you swear you just saw the exact same pony not five seconds ago somewhere completely different?

Of course you have. Everypony has encountered an Outsider at some point. But never up close, it's always at a distance, and they're always gone before you have the chance to challenge them.

But sometimes the rules get broken. Sometimes fate gets distracted for a moment, and a lone unicorn mare gets to see something that she was never meant to see.

Twilight Sparkle's day is about to get very weird.

FAQ and Supplemental Materials (Potential Spoilers for new readers)

Featured! Twice!
...I really don't know what to say!

Special Thanks go to Horizon for initial proof-reading, editing, and signal-boosting, provided as a prize for spotting an Easter egg in his story Hard Reset II. Seriously, it's an awesome, brain-warping story and you should go read it right now.

Thanks also go to my editors for putting up with my atrocious grammar and spelling errors - Ganelon, Ephraim Blue, BronyWhooves, Commonancestry, Princess Autumn Forest, and Morning Sun

Cover art credit goes to EMedina13 and tamalesyatole. I am looking for more appropriate art, so If you think you can do better, let me know.

Princess Celestia has trained her three apprentices, Sunset, Trixie and Twilight, to become the newest generation of the Knights of the Realm, protectors of Equestria. Their abilities and morals are unquestionable, and they're also perfectly willing to become the heroes Equestria needs. However, something had to give, and in the process of turning them into the future Legendary Heroes, those three ended up becoming particularly eccentric in their methods and quirks. This is the start of a very silly era of heroes.

October 2019 Edit: The story's rating has been changed from E to T.

Sunset Shimmer ran through the mirror seeking two things: an escape from Celestia, and a way to get revenge. Meeting up with these strange creatures called "humans," she can say with confidence that she has accomplished the first of her tasks.

Now a student of Mahora Academy, Sunset, or Nichibotsu Hikaru as she's now called, must navigate the overly eccentric life of class 2-A, all the while keeping an eye out for any signs of magic. After all, how is she supposed to take her revenge without...

Wait, what do you mean their teacher is only ten years old!!!

(Familiarity with Mahou Sensei Negima is not required to understand this story, but it will definitely help.)
(Featured since June 26, 2018.)

The war is finally over. We ponies have lost. Our plan to convert humanity into ponies has failed. Hundreds of thousands are dead. Homes destroyed. Our nation is shattered and near annihilation. All because we underestimated humanity and their refusal to become like us.

I alone now hold the fate of my people in my hooves against the humans who want nothing more than to destroy us for the so called atrocities we have committed against them. I've lost my friends one way or another. My family. My fellow Princesses.

I have but one duty and that is, reluctantly, to see that we are shown mercy.

I'm just afraid of the cost. Or what I will learn from this.

Based on The Conversion Bureau series.

Pre-Read by bahatumay and Chaotic Note

Edited by Biker_Dash and wlam and Bemmo

Please Help Out The NegotiationsVerse TV Tropes Page

After a fight with Celestia, Sunset flees through a magic mirror into a different world.

Without her horn, any direction in her life, the inability to simply go back home and surrounded by strangers, she has to go on a journey of self discovery to find meaning in her life as dark forces begin to threaten the world she resides in.

But, at least she still has her magic and plenty of instruction manuals to learn more from.

Unhappy that her future as a member of the monarchy is denied by Celestia, Sunset Shimmer escapes through Starswirl's mirror into another world, planning to take it over to prove once and for all she was fit to rule. What she didn't expect—besides a species change—was to arrive in a world already conquered.

TvTropes Page (Just created! Needs Help!)

Art (Will contain spoilers)

Sunset Shimmer - Bloody Sunset

Spoilers Ch. 11+: Angel - Angel and Sunny
Spoilers Ch. 18+: Princess - Comic
Spoilers Ch. 121+: Alejandra Acevedo - Flying at the speed of death
Spoilers Ch. 161+: Apple Bloom - Bloom
Spoilers Ch. 180+: Food - Sunset's Party Dress
Spoilers Ch. 185+: Fugue - Fugue by Rametep
Spoilers Ch. 197+: Exhausted

(Art is always welcome!)

WARNING: CONTAINS SPOILERS FOR THE WHOLE STORY: TIMELINE