Story One of the Origin of Harmony series.

Following the events of the Tirek terror campaign, Twilight set out to stop anymore disasters while they were ahead. She never imagined how deep and complex Equestria's greatest secrets were, nor how they would affect her.
Now, after a series of attacks have left Equestria in tatters, she and her friends and her fellow princesses must pick up the pieces, alongside her fellow ponies. However, this would be the first time most of them would feel wounds this deep, for the fight for Gaia has only just begun.
Written in third person limited. Be weary, for the story is a puzzle; good luck, and pay attention.