Like so many ponies, Rainbow Dash was blissfully oblivious to the secret war raging since the birth of Equestria between The Arcanum and The Assassins. Rainbow discovers that she is descended from The Assassins when she and her friends are pony-napped by The Arcanum, who force Rainbow to relive the memories of her ancestors through a special spell caled "The Animus" so that they can discover the locations of lost artifacts of tremendous power. With these artifacts The Arcanum hopes to rule all of Equestria, and unless Rainbow figures out a way to stop them before it's too late, they very well may.

But as Rainbow relives the lives of her ancestors from the era of Starswirl the Bearded through the reign of Discord and even up through the war against Nightmare Moon, she discovers that something much larger than the freedom of Equestria is at stake, and that the ponies are just pawns in a giant game that very well may result in the destruction of all Equestria.