The Alliance Civil War is an unnamed conflict between the internal factions of the Alliance. Sparked by the AIs of the Defender Fleet going rogue, it required the Alliance Council to bring in the Navy to take down the rogue fleet and the Marines to aid in taking down other organizations and defending against said groups.
As the Alliance-Syndicate War raged on, problems occurred between the Alliance government and its military. Many, if not most, members of the military began to see the government as incompetent, with some like Admiral Bloch planning to launch their own military coups. To counter this, the Alliance grand council began investing in a variety of covert operations over the years. As these operations continued, they began to have virtually no oversight, leading to the council having less and less knowledge of what they were actually accomplishing.
One covert program proposed was the development of a fleet of ships controlled by loyal, glitch-free artificial intelligence, which would be able to counter any attempted coup and never turn on the government itself. However, with the war still ongoing, there was no way for the government to successfully fund such a program, leading to it initially being dismissed. This changed at the end of the war, not only meaning there was less funding needed for the military, but also leading some on the grand council to see John Geary of the Alliance Fleet to be a major threat, as he had both the command of hundreds of ships and the support of his officers, some of whom were already attempting to convince him to lead a coup. For this reason, the AI program was approved and the construction of the "Defender Fleet" began.