The Comprehensive Peace Agreement (CPA), signed on January 9, 2005, was celebrated internationally as the end of Africa’s longest-running civil war. Brokered by the Intergovernmental Authority on Development (IGAD) and a troika of Western nations, it was a complex attempt to create a “one-country-two systems” model for Sudan. In this paper, we argue that while the CPA’s flaws ensured a North-South split, its power-sharing structure was the main reason for the devastating and hegemonic kleptocracies in the internal politics of South Sudan. We contend that the CPA was less a blueprint for national unity and more a meticulously managed, six-year roadmap to creating an ethnocentric state. Its fundamental structural flaws not only made future conflict likely but also inadvertently created the political architecture for ethnic hegemony and state capture within the future South Sudan, a situation that can ONLY be reversed through a new and fundamental paradigm shift.
The CPA’s design contained several deep-seated, fatal structural flaws that undermined its goal of making unity attractive and guaranteed a fractured outcome. The most critical structural failure was in the security arrangements. Instead of mandating the creation of a single, unified national military, the CPA allowed the Sudan Armed Forces (SAF) and the Sudan People’s Liberation Army (SPLA) to remain separate, intact military entities during the interim period. The “Joint Integrated Units” (JIUs), intended to bridge this gap, were never truly integrated, with implementation lagging 18 months behind schedule and hampered by a lack of logistical support. This “two-army” provision ensured that the ultimate arbiter of any political dispute would remain a military force, not a democratic negotiation. It institutionalized mistrust and maintained the command structures that had prosecuted the war for decades.
The agreement systematically deferred the most contentious issues, creating ticking time bombs. The status of the Abyei region was to be decided by a separate referendum that was never held due to disputes. “Popular consultations” meant to address grievances in South Kordofan and Blue Nile were similarly suspended or failed, leading to renewed conflict in those regions. Furthermore, the democratic institutions envisioned by the CPA in the Southern region remained untested. National elections were delayed until 2010, when the national focus had already shifted entirely to the 2011 referendum on independence. This meant the Government of National Unity was never legitimized by a truly national democratic mandate, functioning instead as a fragile coalition of two parties waiting for the clock to run out. The SPLM’s temporary withdrawal from the government in 2007 over these implementation failures was a sign of the agreement’s profound instability long before secession.
While the CPA’s flaws ensured a North-South split, its power-sharing structure had a devastating and lasting impact on the internal politics of South Sudan. It concentrated immense power in the hands of a single movement, laying the groundwork for the violent kleptocracy and ethnic conflict that would engulf the new nation. It was fundamentally a bilateral pact between two entities: the National Congress Party (NCP) in Khartoum and the Sudan People’s Liberation Movement/Army (SPLM/A) in the South. This framework effectively handed the entire political, military, and economic apparatus of the semi-autonomous Government of Southern Sudan (GoSS) to the SPLM, marginalizing other southern political voices and armed groups, a characteristic deeply manifested today. The agreement’s wealth-sharing provisions, which directed 98% of the GoSS budget from oil revenues, funnelled immense resources directly to this SPLM-dominated administration. This created a system where political power and access to state resources were the same, controlled by a single party.
At independence in 2011, the SPLM political elites did not create a pluralistic democracy but instead installed a system of violent kleptocracy, where corruption became the foundation of government. With the external adversary in Khartoum gone, the internal factions within the SPLM began a violent contest for control of the state itself. The winner-take-all political system, inherited from the CPA’s structure, incentivized this struggle.
This internal power struggle quickly fractured along ethnic lines. Two years after independence, a political crisis between the President and his Vice President erupted into a full-scale civil war in 2013, and then in 2016, to a final control involving house arrest in 2025. The conflict saw forces on all sides targeting civilians based on their ethnic identity. By centralizing power within a single movement and by omitting requirements for internal democratic checks and balances, the CPA created a system where the struggle to control the state would inevitably manifest through ethnic violence. A similar incident occurred in Khartoum between the President and his deputy, though the deputy president evaded arrest.
The legacy of the CPA is, therefore, twofold. It successfully managed the peaceful secession of South Sudan. Still, it did so through a framework structurally incapable of fostering unity and simultaneously created a hegemonic, single-party political system in the South. The parallel and interlocking state failures in both Sudan and South Sudan have reached a terminal stage, rendering the two-state status quo not only unsustainable but actively catastrophic for their populations and regional stability. This system, rich with oil money but devoid of proper governance and accountability, has collapsed into a devastating ethnic civil war, proving that the CPA had not solved the root causes of conflict but had merely shifted them south of a new border or, at worst, divided the problem into two demographics.
Dr Ayine Nigo is an author and lecturer at the University of Westminster, London, United Kingdom. He can be reached via nigoayine@gmail.com.
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