Tensions were further inflamed by the unresolved issues lingering from the secession of South Sudan. Although some progress had been made with minor-level matters, such as a September 2011 agreement on opening several border crossings, the issue of oil revenue sharing—specifically, coming to an agreement regarding how much money South Sudan should pay Sudan for the use of Sudanese pipelines and port facilities to transport and export its oil—was quite contentious. South Sudan pointed out that the fees Sudan was demanding were as much as 10 times greater than the average rates paid by other countries in similar situations and refused to agree to the inflated price. In the absence of an agreement, in December 2011 Sudan began confiscating South Sudan’s oil to make up for what it claimed it was owed for the unpaid transit fees since the July secession. Ongoing talks to resolve the issue, led by the AU and held in Addis Ababa, Ethiopia, were not successful, and in January 2012 South Sudan began shutting down operations in its oil fields to prevent Sudan from taking any more of its oil. The action proved damaging to the economies of both countries but especially South Sudan, which relied upon oil revenue to fund almost its entire budget. Meanwhile, South Sudan investigated alternatives to Sudan’s oil pipelines and exporting infrastructure, including the construction of a pipeline through Kenya and another through Ethiopia and Djibouti.

A series of agreements addressing oil fees, borders, and other issues, signed by both countries in September 2012, initially appeared to resolve the standoff, but in reality it continued for several more months because of dissension between the two countries over how to implement some of the terms agreed upon. Talks continued, however, and bore progress when a commitment to implement the September 2012 agreements, with specific deadlines attached to the necessary actions, was signed in March 2013. South Sudan resumed oil production the next month.

In the midst of the oil troubles, another high-profile issue—the unresolved matter of border demarcation—also led to many skirmishes and at times appeared to bring South Sudan and Sudan to the brink of war. Such was the case with the high-profile battle that began in March 2012 over Heglig—an area that was, pending final demarcation, generally recognized as part of Sudan and home to one of Sudan’s most-important oilfields, although South Sudan also laid clam to the area. After South Sudan suffered repeated aerial bombardments and ground assaults launched by Sudan, South Sudanese troops occupied Heglig for several days in April, ostensibly to stem further attacks into South Sudanese territory, before withdrawing from the area after bowing to pressure from the AU and UN, which held South Sudan’s occupation of Heglig as illegal. Fighting in the area continued, though—as did Sudan’s aerial bombardments of South Sudanese territory—and grew to include the hotly contested Abyei region before finally subsiding in May, as both countries began withdrawing their forces from the region.

The status of the Abyei region remained a point of contention. In the absence of the long-awaited referendum that was to determine whether the region would be part of Sudan or South Sudan, the South Sudanese-aligned Dinka residents organized a nonbinding referendum that was held in October 2013, in which 99.9 percent of the voters opted to join South Sudan. Notably, the Abyei residents aligned with Sudan, the Misseriya, did not vote. The referendum and its results were not internationally recognized.

Domestic problems

Within South Sudan the government was faced with escalating ethnic violence, particularly between the Lou Nuer and Murle peoples in the Jonglei state, with cattle rustling being one of the main issues, as well as a seemingly endless string of retaliatory attacks that killed more than 1,500 people and displaced tens of thousands in the years following independence. The new government also had to deal with rebel activity from several groups active in Jonglei and other states, which also was closely related to ethnic divides. Amnesty offers from the government to the many rebel groups met with mixed success.

Signs of growing dissension within the ruling party, the SPLM, were evident throughout 2013. Kiir dismissed his entire cabinet in late July and shortly thereafter unveiled his new cabinet, which was smaller. Riek Machar, who had served as Kiir’s vice president, was not retained. Meanwhile, Machar voiced his ambitions to challenge Kiir for SPLM leadership and to be the party’s presidential candidate in the country’s 2015 elections, as did Pagan Amum, another dismissed cabinet member also seen as a political rival of Kiir within the SPLM.

The simmering tensions came to a head on December 15, 2013, when gunfire erupted between troops loyal to Kiir and those loyal to Machar. The nature of the incident was not clear, but Kiir attributed the violence to being part of an attempted coup, led by Machar. Machar denied the coup allegation and, in turn, accused Kiir of using the violence as an excuse to attack his political adversaries. Machar, however, soon emerged leading a force of rebel soldiers, known as the SPLA in Opposition (SPLA-IO; aligned with the ruling party splinter group, the SPLM-IO), and called for Kiir to step down. Tensions were ignited between Kiir’s ethnic group, the Dinka, and Machar’s ethnic group, the Nuer, and violence quickly spread to the civilian population. Fighting intensified, and both sides were accused of having committed human rights abuses.

Regional mediation efforts, led by IGAD, did not make any lasting progress. Beginning in January 2014 and continuing into 2015, several cease-fire agreements were signed, but they were quickly violated as fighting continued. In February 2015 it was announced that the elections scheduled for later that year, in June, would be postponed because of the unresolved conflict. To that end, in March both houses of the legislature passed a bill that extended the terms of elected officials, including the president and national legislators, for three years; the bill was later signed into law by Kiir.

Meanwhile, there was a growing humanitarian crisis in South Sudan, with the ongoing fighting leaving at least 10,000 dead—some estimates were considerably higher than that—and more than 1.9 million displaced a year after the conflict started. Although a famine in 2014 was narrowly averted by donor aid, there was still an increased threat of food insecurity for the population, as the fighting had disrupted farming efforts.

In August 2015 Machar and Kiir, under pressure from the international community—particularly Kiir—signed another peace deal. It called for a permanent cease-fire and the formation of a transitional government and also laid out a fragile power-sharing arrangement. Machar was to return as a vice president in the new transitional government. But, as with previous agreements, both sides violated some of the terms, and fighting continued. One particularly contentious issue was Kiir’s announcement in October that the number of states would change from 10 to 28; such an increase would interfere with the highly sensitive power-sharing arrangements outlined in the peace agreement. In spite of much criticism from all parties involved in the peace process, Kiir implemented the new state structure in late December 2015.

In early January 2016 the government and rebels and other parties agreed to an arrangement for sharing ministerial portfolios in the transitional government, with an implementation date of January 22, 2016. The government was not formed, however, as there were still unresolved disagreements, including that of the contentious new 28-state structure. Meanwhile, in March the UN issued a report describing widespread human rights abuses committed by both sides during the ongoing conflict, with the government-aligned forces being noted as having been responsible for more of the violations within the previous year. The horrifying attacks on civilians included killing, sexual violence, and the systematic destruction of towns, including the deliberate targeting of hospitals, UN bases, and churches. The authors of the UN report declared that the violations they had documented could amount to war crimes or crimes against humanity.

Eventually, Machar announced that he would return to Juba on April 18, to take up the position of first vice president in the new transitional government. His return, however, was repeatedly delayed because of actions by the South Sudan government as well as the rebels, much to the consternation of the international community, which had lost patience with both parties. Machar finally arrived in the city on April 26, 2016. He was sworn in as first vice president shortly after his arrival. Machar and Kiir then set upon the task of implementing the transitional unity government.

In the midst of the domestic troubles, there were some positive developments on the international front. In the last few months of 2015 and in early 2016, relations with Sudan showed improvement and included the reopening of the two countries’ shared border in January; it had been closed since 2011. In March South Sudan learned that it would be allowed to join the East African Community (EAC), a regional trade and development bloc. The country was formally admitted to the EAC the next month.