By the time Captain Markan realized Earth was losing the war against the Znu, it was too late. Earth's shield fell and the Znu scorched the surface to an irradiated wasteland. In desperation and for the survival of the species, she sent Earth's massive worldship on a decade-long journey to uncharted space. Their destination was the fringes of the galaxy, where there was a chance to gain a foothold and grow in strength again, and perhaps find new allies for the fight against the Znu and Decima empires. Learning of this plan, the great empires sent their own worldships, following Earth to the edge, determined to stake their own claim and win the war for the fringe.

In Empires of the Void II, each player has been given command of a mission by an alien empire to establish a foothold at the fringe of the galaxy. The game begins when their massive Worldships reach the fringe, where they must explore, wage war, use diplomacy, and construct buildings to gain victory. The fringe is sparsely populated, and many of the sentient species here are struggling to survive, leaving huge regions of planets open for exploration and colonization. Many species are eager to ally themselves with a powerful empire to gain security and stability in a chaotic and difficult time.