(Systems Alliance still have their worlds, just assume that any worlds that also belong to the UNSC are duplicated and moved deeper into Citadel territory.) Also, the Mass Effect relays are still intact, but the UNSC don't have immediate access to it (Their use of the relays is dependant on if they could figure out how to use the Mass Effect tech). The UNSC has all of her colonized worlds, as do all of the Mass Effect races. All Citadel forces, from Salarians and Asari to the Systems Alliance are pitted in a war against the UNSC. So the UNSC and Citadel (At the height of their power, before Mass Effect 3) are at war.
