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.

The fourth great ninja war was over. With Sasuke's help, Naruto vanquished Madara and defeated the Juubi. However, when all was said and done, the two were betrayed by those they trusted most. Fearing the outcome of the toad elder's prophecy, The survivng kages threw Naruto and Sasuke into time and space with the hopes of banishing the two forever. The two however, manage to end up in an entirely new world, giving the two a possible fresh start. Their arrival however, changes the outcome of upcoming events in this world in ways that should never have happened.

It was an ordinary day in Equestria. The sun was shining, the birds were singing and princess Celestia had some free time from her royal duties. Then the explosions started, explosions originating from the Everfree Forest.

Cover art supplied by RainbowDashVegetaFan123

I always wanted to go to Equestria. When I got the chance, I took the deal without reading the fine print. To my surprise, I didn't arrive there as a pony, or even as a human. It seems I get to view this world from a different perspective than what I've imagined.

My name is Echo. I am a Diamond Dog.

-Edited by the one, the only, Nathan Traveler!
-(Cover by Jovial_Shake of fimfiction.net)
-Now featured on Equestriadaily.com!

Both Link and Epona race to fight evil once again, however once they make it to the thing that is behind all the monsters that roam Hyrule, they get a big surprise. Once again, Equestria is threatened by evil and Link is once again called to the line of duty. Isn't he?
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[NOTES]
I will add tags as I go along.
Cover image was made by Aeroflyte on DeviantArt, which can be found here, go check him out.
Now edited by these people: m2pt5 and Crescent Quills!
Based off of the Ocarina of Time timeline (which includes Majora's Mask), but takes a few aspects from Twilight Princess.
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Spartans never die, they're just missing in action. This has never been more true for Jorge-052 as, after activating the slipspace drive that was supposed to kill him, he is instead flung into a strange world where war is but a distant memory. Will the aging soldier be able to adapt to this new peaceful planet? Or will his only salvation be found in finding a way back to his own chaotic universe?

(It's my first time, so be gentle)
Now featuring a TVTropes page by Sabo88

Fluttershy has found a new kind of creature in the forest. After tending to its wound, she brings it home with her and decides to keep it as her own. She soon realizes that this creature is more than just an animal and soon finds a way to communicate with it since neither of them speak the same language.

After one of that unexpected turns the life makes the god of peace and his angel end in the kingdom of Equestria. Could this help him finding the peace he wants... or he would show them "True peace"

Special thanks to my editors Heartless99 and The Valeyard for their help, I couldn´t do this story without them, also, thanks The Valeyard again since he had help me getting some ideas out when it was hard or I was unsure. Thanks both of you ;)

Walking with the paws of an ancient predator, a young man finds himself in a strange world. A world where horses are the dominant species, and he’s a very rare and dangerous animal. How will a speechless man turned wolf deal with society? How will he approach ponies? Would he even want to bother speaking to them?

(Love interest is not revealed in any of the current chapters. So don't freak out when you don't see it. I'm also focusing on a very realistic sense of love. This will be a later part of the story when romance becomes truly relevant. Point out ALL errors to me when you see them, even the ones that have been pointed out already, and I'll see what I can do.)

(Special thanks to my EPIC Proof-reader and Editor ultra1437)

What would happen if a third survivor was aboard the Forward Unto Dawn? What if this survivor just happened to mysterouisly arrive to Equestria? We will follow the tale of an ODST who happens to survive an unlikely survival during a crash into the royal courtyard, and what happens after that... well, that is for you to read, and find out...

Cover-image provided by VenetianGhost.

Fluttershy is quite the expert on creatures of all shapes and sizes, including ponies. So, as you can imagine, the sight of a walking talking skeleton pony with an afro might give her pause.