In January 2005, the Sudanese government and the southern Sudan People’s Liberation Movement signed a historic peace accord and, in the process, laid the foundation for the formation of South Sudan. The Comprehensive Peace Agreement concluded a 21-year civil war between the parties and sought to restore peace in Sudan. Much of the plan addressed South Sudan’s desire for self-governance. The Machakos Protocol, one of six parts to the Agreement, called for a joint government in Khartoum that involved the SPLM, established an autonomous government in the south and required a referendum on the issue of South Sudan’s independence to be held in 2011.

The lead-up to the 2011 referendum was not peaceful, however, and the relationship between north and South Sudan remained contentious. While the crisis in Sudan’s western region of Darfur did not involve the SPLM, an unrelated conflict erupted in South Sudan involving northern militias. Over the course of several days in late November 2006, heavy fighting occured in the southern town of Malakai between military forces from the Sudanese government and the SPLM. In November 2007, the SPLM later accused the Sudanese government of failing to uphold its duty under the peace accord and briefly ceased its participation in the joint government. The Sudanese government also denied allegations made by South Sudan that in 2009 it supplied weapons to ethnic groups responsible for violent attacks in the south.

Territorial disputes, in particular a conflict over the Abyei oil region, also strained the relationship between the north and the south. Following disagreements over the territorial boundaries of Abyei, which held importance for the referendum and for its natural resources, fighting broke out in the region between forces from the north and the south in May 2008. The parties agreed to seek resolution from the Hague in June 2008. On July 22, 2009, the Permanent Court of Arbitration in the Hague issued an order redrawing the region’s boundaries, and granted the north more control over oil fields in the region.

Despite these disputes, both sides worked towards fulfilling the peace accord and the 2011 referendum by holding [PDF] a national census in April 2008 and agreeing to terms for the referendum in December 2009. In January 2011, the referendum was held and nearly 99 percent of voters favored independence from the north. In February 2011, Sudanese President Omar al-Bashir announced his support for the referendum results and “the will of the southern people,” despite having campaigned against secession. South Sudan joined the ranks of independent nations on July 9, 2011. The new nation continues to struggle with conflicts, however, including territorial disputes with Sudan and rivalries within its government.