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.

Written for the Lunaverse April Writing Event: A burst of magic heralds the arrival of a visitor from another world. While Trixie and her friends know that Corona is somehow behind this, they still must make this visitor feel welcome, even though his mysterious ability makes them more than a little nervous.

As for the visitor...well...he can only think of two words to describe his predicament.

Something is happening in the hallowed streets of Canterlot. A madpony hunts for those he believes responsible for his disgrace, urged on by a mysterious force that gives him terrifying power. Captain Shining Armor of the Royal Guard is in a race against time to apprehend this felon before blood is spilled and lives are lost. And in order to do so, he must turn to an ally that may be more threatening than than the very pony he is pursuing. A story from the Lunaverse, it follows the consequences of Greengrass's Night.

Sweet Apple Acres is ravaged by something mysterious, leaving a blighted wasteland in its wake. Ditzy Hooves is savagely attacked while out making her deliveries. Something mysterious has taken up residence in the Everfree Forest that threatens to overrun Ponyville and even the rest of Equestria. Twilight and the others must race to find a solution to the problem and drive off the menace before Ponyville and beyond are picked clean to the bones by the vicious marauders. (Response to prompt 2 for the February Write Off)

While experimenting, Twilight's new teleportation spell goes awry, sending her careening into a different world, just in time to take part in a fantastic ritual called Heaven's Feel. Twilight must adapt to the world of humans and take part in the vicious conflict that is the 4th Holy Grail War as a Servant alongside her equally reluctant Master. The duo must contend with powerful adversaries and survive the subtle machinations of the Magi determined to win the Grail at any cost. Can Twilight overcome her unwillingness to take the lives of others? More importantly, should she? And is there any way for the displaced Unicorn to return home? Trapped, alone and in a different world and surrounded by enemies on all sides, does the Magic of Friendship still hold any hope for Twilight?

A crossover with Fate/Zero.

The Bearers of the Elements of Harmony encounter the members of a mysterious organization that has been protecting Equestria from the shadows for thousands of years. In their quest to learn more, the Bearers learn hidden truths about Equestria's creation and come into conflict with an ancient conspiracy that threatens to unleash an enemy of unimaginable power.