This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

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.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey