This story is a sequel to Foal of the Forest

Second story of the Savage Skies series:
Dawn Lightwing has overcome many trials in his life; persecution for his unique eyes, living amongst the monsters of the Everfree Forest. But now all of that is behind him. He's been adopted by Fluttershy, mended from his conflict with Applejack, and now sits poised to go to school and live the life of a normal foal. Unfortunately, Dawn's past is not so far behind him as he would like, as his experiences have left scars on his mind and heart that threaten everything he has gained since coming to Ponyville.

Followed by Storm on the Horizon.
Now with a TV Tropes page.

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.