Nimeiri was overthrown in 1985. During the transitional governance period, several half-hearted attempts at peace failed over the question of exempting the South from Islamic law, an unacceptable prospect for many in the central government but something the South insisted upon.
Sudan’s current President Omar al-Bashir – now wanted in the International Criminal Court for war crimes – took power via coup in 1989, installing the National Islamic Front government. His party’s emphasis on incorporating Islam into the country’s political and legal systems further exacerbated the North-South conflict.
Meanwhile, the SPLA/M gained influence, becoming the main voice for South Sudanese. Bashir’s alienation of western and eastern regions of Sudan drove them to the sides of the southern rebels, led by the SPLM/A and united under the leadership of Col. John Garang.
Several agreements were signed between Khartoum and some of the southern rebel factions to end the open conflict between the North and South, but the SPLA was not one of the parties to the agreement.