It started mundane enough. Twilight and Rainbow Dash were dealing with a minor Friendship Problem north of Canterlot; not all too serious. Frankly, something the ponies could have dealt with but the Cutie Map decided otherwise. Dispatched to the Crystal Empire to investigate mysterious disappearances, things swiftly begin to go downhill. In short order, Sombra makes his return and Rainbow Dash is lost to the tyrant’s power whilst he consolidates control. Forced to find a way to stop him without their friendship powers, another of the five is lost to Sombra in short order; now becoming his student. However, even that is not all as it seems as Sombra’s plans now go far beyond conquest. They seek to reshape the very existence of many creatures. With two of its greatest heroes now working for their enemy, and Sombra’s plans slowly coming to fruition, how will Equestria stand against the greatest threat of all?!

Timeline note; You can place it comfortably between "A Horse Shoe-In" and "The Ending Of The End-part I."