Ground Control II: Operation Exodus takes place during the year 2741 AD, roughly 300 years after the events in the original game. The democratic and freedom caring Northern Star Alliance (NSA) is being hard pressed by the warmongering Terran Empire. The war has recently entered a new stage; a brutal and deadly ground war, as the Empire has managed to land their first troopships on the last NSA controlled planet Morningstar Prime. Captain Jacob Angelus, a battle-hardened officer in the NSA armed forces, finds himself becoming the central figure in the war against the Terran Empire. The situation is desperate and for the NSA destiny is at hand; its only hope lies in an ancient legend.