In 2003, two rebel factions, the Justice and Equality Movement (JEM) and the Sudan Liberation Army (SLA), revolted against Khartoum.

The Darfur Peace Agreement was signed in 2006, between Khartoum and the SLA arm led by Minni Arkou Minnawi. JEM and Abdelwahid Muhamed El Nur’s SLA contingent refused the peace deal, with El Nur asserting that the agreement did not include or respond to crucial needs of the Darfur population. Upset over the accord created a critical change in the nature of the conflict. What had predominantly been a direct battle between rebels and central government, then included opposition groups warring against each other as well.

JEM is the only opposition group to launch assaults on Sudan’s strong political regions. In 2008 JEM raided Omdurman, where the parliament is located, and it has also attacked oil installations in Kordofan.

In March 2009, an arrest warrant for President al-Bashir was issued by the ICC for war crimes and crimes against humanity in Darfur.

The war has crossed heavily into Chad and Central African Republic. In January 2010, Presidents Idriss Deby of Chad and Omar al-Bashir of Sudan agreed to stop supporting each other's rebels.

All of the armed movements hold that no settlement can be reached unless Darfur is restructured into a single state. It was separated into three regions in 1994, the divided states being North, South, and West Darfur. Within Darfur, this is commonly believed to have been done with intentions of weakening the territory. In March 2011, the government announced a plan to construct two new states out of the region, to be Central Darfur and Eastern Darfur. This has enraged rebel groups who claim it as a ploy to further divide and cripple Darfurian efforts.