The Comprehensive Peace Agreement failed comprehensively to bring peace to Sudan. The neo-liberal mediators of the international community can be only partially blamed for failing to understand the root causes of war, but in the end only the Sudanese can make peace among themselves. The failure to resolve post-war issues in the immediate postreferendum period contributed to continuing instability in both nations: the continuation of war in Sudan's new south, and the outbreak of new war in South Sudan. For a brief time each government believed it could bring down the other by supporting cross-border armed opposition. They succeeded only in interlocking their respective civil wars.

A deadlock over border issues and oil revenues dominated relations between the two nations for the first two years after South Sudanese independence. They converged briefly in 2012. At the beginning of the year Sudan seized South Sudanese oil, claiming compensation for alleged non-payment of fees, and South Sudan shut down the pipeline. Then, in response to cross-border attacks into Unity state from the Sudanese air force and a dissident group calling itself the South Sudan Liberation Army based in the oil field of Panthou/Heglig, the SPLA counter-attacked, seizing control of the oil installation when the SAF unit protecting it fled. Rather than withdrawing its troops immediately, having made the point about Khartoum's subversion, Juba continued to occupy the base until forced to withdraw following the combined pressure of diplomatic censure and SAF's return in strength.

Tension continued elsewhere along the contested border, especially in Abyei when the Ngok Dinka paramount chief Kuol Deng Kuol was murdered by the Misseriya. Frustrated by the lack of mediated progress the Ngok Dinka held their own referendum in October 2014 and voted overwhelmingly to join South Sudan. The Misseriya did not vote because the Misseriya were not there, their claim to ownership of the Abyei area resting on their seasonal use of dry season pastures. Neither Khartoum nor Juba recognized the referendum result.

Wars in Sudan's New South

The war in South Kordofan and Blue Nile, which began in 2011, followed the seasonal pattern of fighting established during the 1983−2005 war. Government dry season offensives aimed very largely at disrupting the civilian subsistence economy alternated with increased SPLA-N activity during the rains.