The precise duration of the conflict is not clear, but the Colonies were hanging on by a thread by 2311, suffering from dwindling resources and public support for the war effort. In a bid to regain the upper hand, the Sovereign Colonies launched a covert Galactic Expedition to Tau Volantis, committing a substantial amount of ships, men, and materiel to unearthing the secret of the Markers and what the Colonies believed to be an inexhaustible energy source that would turn the course of the war and history.
The Expedition included elements from the Sovereign Colonies Armed Forces that had experience in black ops against Secessionists during the riots on Earth (163rd Reaper Unit), supply line raids (the famed Marauders), and special operations forces (UN14), on top of a generous crop of fresh draftees and conscripts.
The expedition became the death knell of the Colonies. The discoveries made on Tau Volantis revealed the Markers to be an existential threat to humanity and the Council invoked Scenario Five, purging all material and personnel related to Marker research while burying what couldn't be destroyed. The extent of the purges nullified the ability of the Colonies to wage war, leading to a Secessionist victory in short order.
The Secessionists seized power in the vacuum left by the Colonies, establishing Earth Government Colonial Alliance, a centralized government with Earth at the core. The widespread scuttling of SCAF ships as part of the purges led to the perception that the Colonies were implementing a scorched earth policy, unwilling to turn their assets over to the victorious Secessionists..
- In the beginning of Chapter 3 upon entering the Roanoke if the player immediately exits, Isaac will call Norton asking about S.C.A.F. and the flotilla and Norton will start talking about the secession war and give his opinions about S.C.A.F.