Sudan's Stake in the Conflict

Facing pressure from the Ugandan military, the Lord's Resistance Army (LRA) has used southern Sudan as a base for launching attacks since the mid-1990s. For most of the decade, the LRA received military support and safe haven from the Government of Sudan. In exchange, the Khartoum-based regime used the LRA to destabilize the southern region and fight the southern Sudan People's Liberation Army (SPLA), who in turn was funded by the Ugandan government. The 1999 Nairobi Agreement between Sudan and Uganda supposedly ended these proxy relationships. However, covert assistance still persists, particularly from elements in the Sudanese armed forces to the LRA.

Sudan's 21-year war caused more than two million deaths and the displacement of over four million people, including over 230,000 Sudanese refugees who still live in Uganda. In July 2002, with crucial support from the Kenyan and U.S. governments, the parties signed the breakthrough Machakos Protocol. This outlined an agreement granting southern Sudan semi-autonomous status and a 2011 referendum on secession.

Subsequent negotiations led to the Comprehensive Peace Agreement (CPA), signed in January 2005. Since, the new semi-autonomous Government of South Sudan has been eager to consolidate control over its territory. However, the persistence of the LRA poses a significant obstacle. LRA activity, including looting, abductions and killings, expanded in scale and frequency in 2005. Many fear that the Sudanese government could again use the LRA as a proxy militia, this time to prevent the 2011 referendum and maintain access to the rich southern oil fields. Clashes in November 2006 between Sudanese armed forces and the SPLA may foreshadow a return to civil war.

The Government of South Sudan, foreseeing such threats, presented the LRA with an ultimatum in late 2005: negotiate or be expelled by force. Facing growing international pressure, the LRA accepted. In July 2006, the Government of South Sudan began mediating peace talks in Juba between the rebels and Ugandan government. By August, the parties reached the breakthrough Cessation of Hostilities (CoH) Agreement, bringing relative calm to the region. However, violations by both sides and mistrust have delayed negotiations. Many also fear that Khartoum may disrupt the process to undermine the Government of South Sudan. Without greater international engagement and leverage, this historic opportunity for regional peace may collapse. A return to violence in northern Uganda could spell doom for the CPA.

Meanwhile, the outbreak of violence in Darfur since 2003 has added another dimension to regional instability. Responding to rebel uprisings in February 2003, the Sudanese government began indiscriminate aerial bombing of the western Darfur region. In addition, they used nomadic tribes as proxy militias to attack villages. In the ensuing violence, an estimated 250,000 people have died and almost 3 million people remain displaced. This includes 200,000 refugees that have crossed into Chad, which could reignite war in that country. The African Union established the African Union Mission in Sudan (AMIS) to respond, but a limited mandate and low numbers have hampered the mission's effectiveness. As a result of widespread grassroots pressure, the international community has focused heavily on Darfur. Though international policy has not stopped the violence, humanitarian assistance to the area has skyrocketed. Unfortunately, the U.S. and others have maintained tunnel vision in addressing Darfur, overlooking its connection to regional dynamics.

In fact, the conflict in Darfur and instability in southern Sudan are intricately connected, bound by their mutual marginalization from the power center in Khartoum. In both cases, Khartoum has used proxy militias to decimate villages and defuse regional mobilization. Lasting peace in either region is not possible unless the international community faces these connections. The broader regional instability that feeds these two conflicts also speaks to the need for a coherent regional strategy. The fluidity of borders, proliferation of insurgent groups, failures of governance and persistent war economy cut across the region. Only a regional strategy of peace processes and peacekeeping will break this cycle of violence. Support for the historic Juba peace talks, combined with implementation of the CPA, can provide a foundation for a comprehensive regional approach.