The League Civil War was a war that occurred way back in the Dark Times, before the League was properly established. In those Dark Times, the Members of the League refused to co-operate or compromise, and the Council Meetings were little more than petty squabbles. Even the renowned Face of Boe couldn't stop races like the Daleks and the Reapers from getting at each other over border controls, supply distribution, and most importantly, restrictions on military action.
Eventually, war broke out. The more aggressive races had already begun mass-armament and League sanctions and diplomatic action could do nothing to prevent the inevitable warfare. For the duration of this time, the major planets of the League became decimated, each and every one torn apart by war. Despite only having existed for a short time, (relatively speaking), it looked as if the League was going to collapse in on itself.
Thousands upon thousands of Daleks, Reapers, Sith, Jedi, Cybermen, Elites, Brutes, Jackals, Flood, Protheans, Turians and even Hanar waged endless war against each other. The citizens of the Galaxy stirred, knowing that the outcome of the war would decide their fate. Several star systems broke away from the League altogether and founded what became known as the Galactic Council - races like the Mole Men, the Money Spiders and the Prowlers.
When all hope seemed lost, there was some degree of improvement. The Sith Empire collapsed and was rebuilt as the Galactic Republic, and at the same time a Turian-Cyberman alliance shattered the Dalek fleet in orbit around their home planet of Skaro during the Battle of Skaro at the end of the Dalek-Turian War, and the Dalek Emperor was killed. However, this was later overturned when the War reached its climax around Inon II, the capital of the League, and the massive Battle of Inon II took place there which ravaged League society. The Face was eventually able to establish order by disabling the aggressor ships, and a peace treaty was drawn up.
At this point the Hanar religion had been established and they agreed on a non-violence policy. The most aggressive races such as the Flood and the Reapers and even what was left of the Daleks retreated into the Dark Space outside any Galaxy and this left only the Covenant as aggressors. The negotiations were short, but in the end the Covenant were cast out to the far reaches of the Galaxy, beyond the reaches of the Council, the League or the New Republic. This allowed them to rebuild their own personal Empire years later, but they would not return until they waged war against the newly-emerged Human Empire, 2500 years after the League Civil War.
In the aftermath, a severe reordering of the League was instigated. The various feuding alliances were disbanded and they were all reintergrated back into the League, except for the 'Forgotten Twenty', being the races or societies that were cast out of the League following this conflict. The most prominent are as follows:
- Daleks, later reintegrated into the League under the Parliament of the Daleks, centuries later
- Cybermen, later reintegrated into the League following the Cyberman-Borg War
- Reapers, later reintegrated into the League after promising reform
- Covenant, later reintegrated into the League after the Human-Covenant War
- Mole Men, later reintegrated into the League after the Great Credit Crunch
- Money Spiders
Despite this enormous setback, with some of its most powerful members having been excommunicated, the League maintained its position as largest peacekeeping force in the Galaxy, and there was not another conflict in the Galaxy of this scale for another 5000 years.