When Twilight is placed in charge of the Equestrian government's first line of defense against alien incursions, she finds herself housing a dangerous entity within the castle. However, the question remains; why did it come to Equestria?

The primary divergence from the 'canon' story-line is probably the exclusion of Discord and an incredibly fuzzy knowledge of anything beyond season 3.
The story gets darker as it progresses; be forewarned.