First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

This story is a sequel to The Promise of a New Day

Story three of Savage Skies:
All sorts of things are brewing in the pegasus city of Cloudsdale, which is a problem for Ponyville as the one thing that isn't is a rainstorm. As the drought continues to drag on, Rainbow Dash must confront her hometown and its history, as well as her own history. But she won't do it alone, which is good, because she'll need all the help she can get.

Series starts with Foal of the Forest.
Now with a TV Tropes page.

This story is a sequel to Storm on the Horizon

Story 4 of the Savage Skies series.

It is well-known that the brighter the light, the deeper the shadow. Princess Celestia is unquestionably Equestria's brightest guiding light. Unfortunately, two ponies must deal with the very deep, very dark shadows that she casts.

Dawn Lightwing has overcome many trials since moving to Ponyville. However, his past and the ponies that haunted it are not as far behind him as he would like to think. Whether he likes it or not, his enemies, who draw their hatred from their irrational reverence for Princess Celestia, have found him again and he must struggle with the fact that his mere presence could a threat to his friends and his new family.

Twilight Sparkle must deal with a different shadow as she travels to Canterlot in order to learn more about the mysterious Eyes of Nightmare, as she must contend with the Noble Court, who live in the shadow of the Royal Palace itself, its members planning to use Twilight and her friends to advance their own ambitions, stopping at nothing to have her under their influence.

Thankfully, neither of them will have to deal with these obstacles alone.

However, something even more dangerous is stirring. Dark matters are afoot.

The series begins with Foal of the Forest.
Now with a TV Tropes page.

Book II
Brought out of the darkness of solitude and into the light of friendship, Dusk returns once more to see and learn just what magic and wonder friendship has in store for him. Once thinking he was the most useless, pointless pony to ever exist, he has now found those who care for him and appreciate him for who he is, opening up new possibilities never even considered.
He will join the girls on their adventures and experiences with friendship’s magic, helping them along as they go, having a few of his own and learning and discovering new aspects of himself that become open now friendship is known to him. Along the way, he will also make new friends, challenge his own beliefs and convictions once more and just discover how much more wonderful life is with friends as a part of it.
But that’s not all that concerns him here. He needs to do something different about himself, but what? He has his colour magic, but where exactly did it come from and are there others he shares it with? Twilight may be his best friend but… what’s this new feeling that he has when he’s around her now?
All of this will be explored, as Equestria prepares to see a brand new Dusk.
Cover again by Quillin Words.

When John suddenly finds Luna's cutie mark on the side of both his thighs, a chain of reactions begins that is as far as he knows, irreversible. Are there any other people that are changing? Or is he completely alone in this world?
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Luna branch of the 'Five Score Divided by Four' universe. This story deserves a read as it is where this all started.
Credit for cover picture (Night Time) goes to Aeritus91
Collabing with: Total Eclipse of the Sun and Experiencing the Dusk

Starfall is a pegasus with a past he would rather forget, and a future that does not appear to even exist. His only true talent is a gift and passion for the stars and the night sky, a passion he has cultivated since he was a small colt. So when he learns of a chance to make this hobby a lifetime career, he travels all the way to Canterlot, desperate to make something of himself.

But during this opportunity, Starfall talent for reading the stars draws the attention of several ponies, including Equestria's royalty, and the alicorn who created the night sky he is so fond of; Princess Luna. What had started as a chance for a better life turns into an opportunity he could never have imagined, as the Princess of the Night begrudgingly takes him under her wing, teaching him all there is to know about the night.

But as Starfall adjusts to this new world he has been thrown into, complications rapidly begin to arise. Can the young, introverted pegasus learn to cope with the fame his new position will thrust upon him? Can anypony break through his defences, and bring out the pegasus he was always meant to be? And can he keep a secret from the Princess of the Night herself, as his feelings threaten to run away from him?

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

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)

When Rainbow Dash's newest trick backfires spectacularly, she and Fluttershy find themselves stranded in the middle of nowhere. Together, they'll have to survive and find their way back to Equestria and Ponyville...no matter how far the journey.

Now with a Spanish translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-1-3-857109863

(Originally submitted to Equestria Daily)
Art by katwalk.

When I was young, I woke up in the Everfree. I couldn't remember my name or where I came from before waking in that cursed forest. All I could remember was hunger and the need to hunt. Yet I travelled with a filly I should have turned into a snack. The only thing that held me back was that she held a clue to my missing past.

Danger surrounded us in that evil place; a pack of wooden wolves, an angry dragon, little blue flowers with a twisted sense of humour, and something else even more terrible than the rest combined. But the biggest threat of all lay hidden in my past. After all, what is worse, the threat you see coming, or the one that you trusted?