Stratospheric Citadels are enemy buildings now?
...were the survivors from the last game made the evil overlord now? =o
It sort of makes sense. Once the winds were driven back and the overlord's threat eliminated, they no longer had to cooperate and work hard to survive. The survivors begin to become more independent and form multiple factions that fight over the land that is now available for taking. Weaker survivor groups are eliminated and the stronger ones begin to subjugate the remainders, taking control of the Stratospheric Citadels, Overlord towers and so on, essentially becoming that which they once fought against.
Of course I doubt this is actually what happened, but hey.