It can be the Core, the Outer Rim territories, or the planets of the Ciutric Hegemony. With the Emperor defeated(for now), your focus will be on securing your main base of operations. The game takes into account the basis behind Imperial navy and army doctrine and not understanding how to properly build your fleets and conquered planets will net you a bad game. IdeologyOne of the most important aspects of taking control of the Empire is understanding its ideology.
