After an attempt on Twilight Sparkle's life at her coronation, former Princesses Celestia and Luna decide to call in an old ally to defend the ruler of Equestria. Even with Twilight's protection, a new force rises to challenge the new ruler.

An ominous and powerful figure named only as the Author leads these insurgents, and his follower's brutal and immoral attacks leave Equestria scarred. However, as time passes, a group of the followers begin to see the fault in their actions.

Having been called from it's slumber, the protectorate of Equestria's newest leader begins to have visions of its past and of its future. Haunted by previous failures, the silent being contemplates its true meaning in the land, and why it really fights for the equine's safety.

Edit: Since I'm only allowed five character tags, I will add more down here. Sex tag for heavy innuendo and nondescript.
Royal Guard
Princess Cadence
Shining Armor
Flurry Heart
Starlight Glimmer
Sunburst
Discord

Alternate Universe starts with the coronation, meaning that everything that has happened in the show is also cannon to this story.