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 Assassination of Twilight Sparkle

A single life can affect so many others in such positive ways, but when it dies all are left to feel the aftermath. With the death of Princess Twilight Sparkle, assassinated at the hooves of both guards and nobles, a nation struggles to recover as the effects of her death are felt throughout Equestria.

The many lives that she had touched will never be the same. Each is their own story of their struggles, their sorrows, and their attempts to move on in the aftermath of tragedy.

(This story is complete!)

***

The one shot series sequel to The Assassination of Twilight Sparkle, that was inspired by the fanfic Ripples by BronyWriter.

Each chapter is about the other characters, outside of Celestia, who deal with the aftermath of Twilight's death in the first story. Some will be main characters, other minor, others OC. But all of them will be affected, all of them will mourn, and all will have to move on.

Feel free to add to the Assassination TV tropes page

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

You know all those stories about cos-players disappearing? Well this is kinda like those. Jason Hughes was just a normal guy attending a con for the first time. Of course he had to buy that omnitrix replica right? Well now he's stuck in a world of talking ponies and has to learn what it means to be a pony.

**This somehow got on the popular stories list on 8/16/14, which is only a day after I published it. Thats a new one*

**So this got featured on 8/17/14 I have no idea how that happened but thanks everyone!**

Big thanks to m2pt5 for taking on the role of proofreader/editor. Also want to thank DuskShadowBrony for being my other editor.

Midnight Storm has had a hard life. She's wandered from city to city for the past three years, and they've all eventually run her out after they've found out what she is. Against her better judgement, she's placed her last hopes on the small town of Ponyville.

The residents here are nice enough, but when they find out what she really is, will they accept her, or drive her out like all the others? And when Celestia finds out about her, what plans does the Princess of the Sun have in store for the mare?

Cover image by Valkyrie-girl

Story now included in The Goodfic Bin

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?

Twilight is about to have her hooves full. Who is this newcomer on the edge of town? AND WHY DOES STUFF KEEP BLOWING UP OVER THERE!? What is with the strange shifting star patterns high above? Join Twilight and friends as they discover that a whole new universe of alien life lies out among the stars. They make new friends and acquire new power. But there will be suffering also, for some things the universe holds are not for the faint of heart.

Because war..... war never changes..... no matter where you are.

If you like Halo AND MLP:FIM you may wanna keep reading

Events in this story take place after the events of Halo 4 Spartan Ops, but before Twilight becomes an Alicorn.

(please note, im juggling a few things, so this story may take me a while. But i figured, what the hay? how else can i spend those free hours in my week?)

Disclaimer: I do not own MLP:FIM or Halo and this story is not an official continuation for either franchise. The real owners are Hasbro, Bungie, Microsoft Studios, and 343 Industries. Give them due credit for the characters, locations, and starships they created.

(Status Update 12/29/2014): Sequel status in doubt. Although considering renaming the sequel based on the name of a song from the band Muse and the song itself (source of some inspiration) I'll let you guys guess in the comments page below the sequel what song inspired me to give the sequel more time and basically, you know, give it a chance. :)

A surprise storm shatters reality for several hundred young college students. Follow the actions of the members of a small, but dedicated group of people as they strive, compromise, and sacrifice in the name of survival and hopefully, a nonviolence truce with those whose nation they have entered.

DISCLAIMER: many of the events depicted herein may cause some anger and confusion. Rest assured that all wrongs WILL be righted eventually. If something does not make sense, feel free to P.M. the author. He will almost always respond.

There are some similarities between this story and the exquisite works that partly inspired this story: A Voice Among The Strangers by Tystarr and also Misunderstandings by The Rogue Wolf. )

Rated Teen for foul language, racial slurs, violence, blood, sexual words and descriptions of sexual organs (but no sexual situations or sexual contact), as well as physical and mental anguish. This is not for children.

Pic is from the Discovery Channel series Survival Of The Fittest.