Equestria is growing, and magical savant Twilight Sparkle is disgusted by the crime and corruption this change has brought. Her life is changed forever when she discovers the Death Note, a notebook with inexplicable and deadly powers. She uses this book to pass judgement on those she deems unworthy of life, aiming to create a perfect world free of crime. But when the two Princesses put their best pony on the case, a mysterious detective known only as L, a psychological game of cat and mouse erupts between the two.
Comments contain spoilers. Artwork by blu-red, opening by Anon3mous. Now with its own TV Tropes page.

A young man with a love of military history and MLP:FIM finds himself dragged into Equestria as war threatens the pony nation.

I got the idea for this story from my Civil War book collection and Altoid's Blood and Guts and Ponies story, as it involves a human coming to Equestria to aid in its defense, partly by modernizing it's military and leading its forces on the battlefield.

Just a warning; the main character is Christian and pro-Union. Just to give people a heads up.

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 human of great power has found his way to Equestria, whether it be fate or coincidence, he is now in a strange magical land of talking ponies. He finds the peace he has been searching for after being called a monster and hated on earth, but his peace will not come easily. There is a terrible threat on the horizon that he will have to face if he wishes to keep the new life he finds.

When Twilight Sparkle slipped beneath the covers last night, everything had been fine. She had friends whom she loved, a teacher she adored, and a bright future ahead of her. But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.

Everything is wrong and nothing makes sense; even her friends have changed. The doctors keep telling her that she is sick, that none of it was real and that it was all in her head. Yet she remembers a life far beyond the hospital walls. She couldn't have made it all up on her own. They must be lying… right?

Ask Asylum Twilight - Still updating regularly!
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Art:
Asylum Cover by conicer
Twilight and Twilight Smiles by dreamingnoctis
Mirror Twilight and Plague Doctor by Jaestring / BloodGoldWings
Twilight Smiles and Doctor AJ by conicer
Nurse Ratchet and Silas and What's in the mirror? by Archonix
Doctor AJ Sketch by Archonix | Colored and vectored version by ReFro82
Twilight's Asylum by Khan the Cake Lover
Smilight by HappySwitch
Twilight Waking Up by Dombrus
Fan Art by toxicdemon10
Asylum Twilight by Madness-With-Reason
Asylum Fluttershy and Asylum Ch 26 by Downburst-Backspace
Twilight and her Twin by v747
Birdgirl by sirValter

Readings and Videos:
Asylum Animated Trailer Video by formuladash
Reading by Gammarobot (SugarCubeRadio): All Chapters Here
Reading by Ender Brony: All Chapters Here
Reading by VisualPony: All Chapters Here
Reading by MelancholyIguana: All Chapters Here
Fan Trailer by Kaidan: Asylum FanFic Trailer Cuckoo's Nest

Sanctuary by Kaidan
Broadhoof Files: Dr. Humors by TypewriterError
Broadhoof Files: Corporal Phalanx Spear (Ret.) by Phalanx Spear
A Hearth's Warming Tragedy by Seven Fates

A special thanks to Breath of Plagues, Rex Ivan,
ChudoJogurt, Cynewulf, Death the Kid, Selbi, PrinceDolph, Blahman2816, Queue, and Gage!

Axan Zenith - Dr. Dreamer
Dratini4 - Way Finder
psychicscubadiver - Bright Mind
Velkaden - Dream Chaser
Reese - Silver Glow
Viola Heartstrings - Clover
Archonix - Spinney Whiteacre

Curious about Five Score? Come check out the story that inspired dozens of side fics and been enjoyed by bronies for years!

Original Synopsis Even though MLP:FiM ended a few years ago, my friends and I still loved the show. Stories, merch, fan art, I loved it all. Things started to get a weird though when I found myself with a cutie mark appearing on my leg. Humans aren't supposed to get cutie marks, so where the heck did this come from? And what's going on with my hair?

More Detailed Synopsis: Five Score is an action/adventure story of the human-to-pony transformation genre. It’s unique from most transformation stories because the transformation itself is not really the point of the story. It’s the inciting incident that raises countless challenges that must be resolved. They are on earth, as a pony, and need to fix this before things get worse. Think about yourself in their hooves for a moment. How are you supposed to change back or even figure out what caused it in the first place? How are you supposed to get food or do anything on Earth without being spotted by humans? If you are spotted or captured, how would you escape? How does one even open a door with hooves!? Did anyone else on Earth get changed as well? How could you get the word out to the other ponies who are themselves hiding? Is it worth risking travel across the country to reach the others? Which of your friends would you trust to help you deal with this? And why did you turn into this particular pony? Surely it wasn’t random chance, right?

These challenges are the tip of the iceberg in this full length adventure novel There’s a lot of humor, many tense scenes, and hell maybe even a war.

But don’t just take it from me, Look what random people on the internet are saying about Five Score, Divided by Four

One of the best things to come out of this fandom.
-IrraticDrop

This made me change how I think about fictional worlds, imagination, and creativity
-relgukxilef

The only story on FimFiction to have me literally shaking with excitement.
-jeramiahsental

SWEET FILLY LUNA I AM FLIPPING MY SHIT RIGHT NOW
-Shadow Reaper

Five Score master editor:
Scrub

Five Score proofreaders:
Comrade Sparkle
Rustle my Jimmies