The Alliance divides its territory into smaller segments in order to better administer it. Prior to the First Contact War, the Alliance divided itself into Sectors consisting of a single populated Cluster, with some Sectors also having newly discovered or less developed Clusters added into their authority, with them later being divided into new Sectors as they are further developed. There were 10 Sectors at the start of the First Contact War, the Local, Acrturus, Exodus, Hyades, Mkali, Apollo, Sereph, Orion, Ginnungagap, and Zeus Sectors. Each Sector has a Division assigned to it constructed from 2 or more Brigades assigned to each Regions. The Alliance Navy generally assigns Squadrons to individual Sectors, but the increasingly thinly spread nature of the Alliance Navy has led to some Squadrons being assigned patrol Regions in multiple Sectors. The Sectors are administered by a Director-General, a rather confusing title considering the existence, at the time, of the Director of the Alliance, a different but more powerful position.

Each Sector is built from several Regions, which each consist of a highly populated world or systems and the surrounding systems to it. Each Region is controlled by a Governor-General, which were originally previous civil administrators hired by the Alliance. However, the Alliance ran out of qualified administrators and turned to a problem it has, a preponderance of mid ranking military officers who joined the Alliance for quicker advancement. The Alliance gave several of these officers, those with more administrative expertise, positions as Governor-Generals, solving both of its problems. An example of this is Governor-General Williams, once a Brigadier General in the United North American States Army with significant administrative and logistical experience, who was quickly given the position of Governor-General over the Shanxi Region.

There are dozens of Regions within the Alliance, each of which is nominally given a Brigade of marines for protection alongside a force of corvettes. However, the Brigades are often understrength, starting out as less than a Battalion and slowly given more personnel as the importance of the Region grows. The corvettes are in an extremely high demand, with many Regions not having enough for their needs.

Below Regions there is no real Alliance authority, with the population controlled by multiple local governments of varying sizes and authority.