The Dark Queen Twilight has just cemented herself as the sole ruler of Equestria. She is extremely powerful, but she wants a power only the Goddess LaurFa had, to see all. To achieve this, she must acquire an ancient relic in a guarded city.
When aliens came, they didn't come from Tartarus, like the ponies were expecting, but from under the sea, and magic couldn't stop them. Luckily our little ponies know something that can: Jaegers. They'll fight to stop The End, and they won't give up.
When Trixie accidentally exposes herself and Twilight to the Bag of Tirek, transforming them both into dragons, dark events are set into motion, and only with the power of her friends and the Elements of Harmony can Twilight hope to save Equestria.
Twilight Sparkle finds herself plagued by frequent Nightmares. Unable to sleep, and believing an old enemy is responsible for her restless nights, she sets out on her own to confront the Darkness, only to fall victim to it.
After being defeated by Nightmare Moon, Twilight is transformed into a puppet of darkness. But when she starts to have flashbacks of a certain baby dragon, she realizes that there may still be hope for Equestria.
With a price on Twilight Sparkle’s head and the shadow of death on her heels, her only hope for salvation is the Magic of Friendship. (Baldur’s Gate Crossover)
Twilight Sparkle has had Runes ever since the Magic Surge when she was applying for Celestia's school, there are powers and a history behind these runes that no pony knows, not even Celestia.