What is the value of a secret? What knowledge lurks forgotten in Equestria's past?

After chasing a thief from Canterlot to the desert mountains south of Equestria, Twilight and her friends are beset by tragedy. To save her friend, Twilight will have to delve Equestria's greatest secrets, and discover a truth that even she will wish she hadn't learned. When the thief's full plans come to light, will Twilight be able to save Equestria's secrets, her friend, or even herself?

Written for the July 2014 Pre-Reader Battle, based on the prompt "The Canterlot Archives hold a dark secret." Contains a reimagining of a G1 villain, but does not require knowledge of G1.