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From Conflict to Cooperation? Sudan, South Sudan and Uganda
From Conflict to Cooperation? Sudan, South Sudan and Uganda
Charting a Way Forward in Sudan’s Unfinished Transition
Charting a Way Forward in Sudan’s Unfinished Transition
Sudan's President Omar al-Bashir (L) welcomes Uganda's President Yoweri Museveni as he arrives at Khartoum Airport for talks during an official visit to Sudan on 15 September 2015. REUTERS/Mohamed Nureldin Abdallah
Commentary / Africa

From Conflict to Cooperation? Sudan, South Sudan and Uganda

When South Sudanese leaders travelled to Khartoum in early June, pragmatically declaring their intent to “normalise relations” with their northern neighbors, it was a tentative sign of hope for what has been one of the Horn of Africa’s worst war zones.

Uganda, historically a staunch ally of South Sudan, is now seeking more constructive relations with Sudan too. The current processes – formal and informal, public and private – tackle a wider set of challenges that have historically inhibited good relations between the three countries. A new understanding between the three could bring a welcome change to the Horn’s complex balance of alliances and animosities.

The new overtures are driven by South Sudan’s economic crisis, coupled with Uganda’s and Sudan’s desire to protect their interests in the country. South Sudan has large oil reserves, which are exported through Sudan, but its production fell sharply with the eruption of civil war in December 2013. With the civil war’s end, Juba now wants to renegotiate the terms of its 2012 oil transfer agreement that mandates large payments to Sudan, arguing that a new deal needs to reflect the global downturn in prices and its own post-civil war financial straits. While Juba wants a new arrangement with Sudan, such a deal would come with strings attached. Donors’ reluctance to bail out South Sudan financially, unless Juba adopts stringent transparency and accountability measures, makes other options seem worse than a wider deal with Sudan.


A new understanding between the three could bring a welcome change to the Horn’s complex balance of alliances and animosities.

Sudan now wants to cooperate too. Its economy, though more resilient, still suffers from the 2011 division of the country, the loss of shared oil revenue, and, like South Sudan, obstacles to full cross-border trade. But in return Khartoum wants South Sudan to help end wars in Darfur and the Two Areas, South Kordofan and Blue Nile, and stop its alleged support for Sudanese rebel groups.

Reaching agreement could be tough but conditions are more favourable than at any time since South Sudan’s secession five years ago. If both sides continue to work seriously on their bilateral relations, chances will rise of resolving other interlinked conflicts, notably the conflict in the Two Areas. A Khartoum-Juba deal would likely limit the operational space of Sudanese rebels – especially the Sudan Peoples Liberation Movement-North (SPLM-N) – and lead to new border security arrangements.

Map showing South Sudan’s historic regions and the border with Sudan. CRISIS GROUP

Khartoum and Kampala’s long rivalry

The territory of southern Sudan (South Sudan since 2011) has long been a site of mutual interventions and proxy conflict between Khartoum and Kampala. During the 1990s, Uganda was suspicious of Islamist Sudan’s apparent desire to expand Arab and Islamic influence southwards. To counter the perceived Islamist threat, Uganda backed the Southern Peoples Liberation Army (SPLA) in the Sudanese civil war. Khartoum supported Ugandan rebel groups, the Lord’s Resistance Army (LRA) and Allied Democratic Forces (ADF), among others.

South Sudan’s 2011 independence directed its neighbours’ rivalry toward competition for influence over the new state. Despite this, Sudan and Uganda have shared interests in common, including unhindered South Sudanese oil production and stability under President Salva Kiir.

Kampala’s concerns have shifted substantially from security to economic.

Sudan needs regular “transit fees” – a per barrel payment for use of the northern export pipeline – to buttress its fragile post-secession economy. Kampala’s concerns have shifted substantially from security to economic. It wants a prosperous South Sudan to trade with, particularly in the Equatoria region bordering Uganda. Kampala also believes it should have influence over major strategic decisions made in Juba; its historical support for the SPLA is reflected in a longstanding defence cooperation agreement, which includes allowing cross-border interventions by the Ugandan army.

When South Sudan’s civil war erupted in December 2013, Uganda deployed troops in support of the embattled Juba government, reviving tensions with Sudan. In response, Sudan provided limited backing to the rebel Sudan People’s Liberation Army – In Opposition (SPLA-IO).

From civil war to regional peace?

The potential for regional contagion following the outbreak of South Sudan’s civil war demanded mediation from the Horn of Africa’s regional security organisation, the Intergovernmental Authority on Development (IGAD). Though it failed to stop the war from escalating within South Sudan in its early months, IGAD’s largely unheralded success was to pull Uganda and Sudan (both member states) back from more aggressive posturing and toward a resolution of the war that both could support.

Critical to the eventual Agreement on the Resolution of the Conflict in the Republic of South Sudan (ARCSS) in August 2015 were key provisions negotiated at the IGAD Head of State level involving Sudanese President Omar al-Bashir and Ugandan President Yoweri Museveni. These included the withdrawal of Ugandan forces – completed in October 2015 – and the “disarmament, demobilisation and repatriation” of any Sudanese rebel forces present in South Sudan, which include the Sudan People’s Liberation Movement/Army – North (SPLM/A-N) and the Justice and Equality Movement (JEM) – which Khartoum alleges are materially supported by Juba. The long-running African Union mediation to end the armed conflicts in Sudan has also engaged both these groups.

Peace in the Sudans is dependent on all three countries’ approach to regional relations.

As the 2015 South Sudan peace agreement recognises, peace in the Sudans is dependent on all three countries’ approach to regional relations. Improved relations between Uganda and Sudan have been reinforced by regional heads of state summits during South Sudan’s peace process, joint efforts to resolve South Sudan’s civil war, presidential and vice presidential visits, mutual disparagement of the International Criminal Court and plans to create a Joint Permanent Commission on bilateral affairs.

Precedents for Cooperation

Despite political will, the inherent complexities of the disputed Sudan-South Sudan border and relationships on both sides make this a fraught process with no guarantee of success. Skepticism and a degree of distrust remain on all sides. Yet negotiators are drawing from past agreements considered a success – notably the Chad-Sudan 2010 agreement, which precipitated the weakening of both Chadian and Darfur rebel groups; and the arrangement between Khartoum and Juba that led to the South Sudan Liberation Army (SSLA) disbanding and its members returning to the South in 2013. Elements of the former SSLA control part of the border as part of the Juba-Khartoum deal, which served both their interests during South Sudan’s civil war.

If Sudan and South Sudan cannot strike a new deal then the broader regional configuration may well revert to its previous state of instability, mutual suspicion and proxy conflict. But the emergence of a new and pragmatic grouping could shift the regional balance of power in the Horn of Africa with significant advantages to the regimes in Kampala, Juba and Khartoum, and help end one of Africa’s most enduring conflicts.

A military officer is carried by the crowd as demonstrators chant slogans, after the Defence Ministry said that President Bashir had been detained and that a military council would run the country for a two-year transitional period, Sudan 11 April 2019. REUTERS/Stringer
Statement / Africa

Charting a Way Forward in Sudan’s Unfinished Transition

Omar al-Bashir is out as president of Sudan, but protesters suspect that the military-led transition is a game of musical chairs. A new curfew raises the spectre of bloodshed. International actors should press vigorously for civilian leadership of a process that must promise further-reaching change.

Late at night on 10 April, after defying the most sustained protest movement in Sudan’s modern history for months, Omar al-Bashir finally lost his hold on power. In an early afternoon announcement on state television the next day, Lieutenant General Ahmed Awad Ibn Auf, Sudan’s defence minister and vice president, confirmed the rumours that had been swirling in Khartoum: the security forces had ousted the president and, he said, placed him in detention. Bashir, who took power in 1989 and was one of Africa’s longest-ruling strongmen, would rule no longer.

Reaction to this news has been mixed. Initially rapturous at the fall of an authoritarian figure whose tenure was stained by major human rights abuses, economic decline and entrenched corruption, protesters soon expressed disappointment at the terms of the handover the defence minister laid out. Ibn Auf announced that a military council would take charge of the country for two years. He also dissolved the government, suspended the constitution and ordered a three-month state of emergency. Many protesters had demanded a civilian-led transitional authority; in their eyes, the regime seemed to be trying to preserve itself under the guise of a coup.

It is thus apparent that the transition remains incomplete. The protesters’ ranks in Khartoum have continued to swell, with campaigners demanding more substantive change. Protester anger was captured in a new slogan declaring that “the revolution has just started”. Where before they chanted the “regime must fall”, thousands of protesters who marched on the streets in sweltering heat after the army announcement declared in a new chant that “the regime has not yet fallen”.

The danger of fighting among disparate armed groups in the event of a chaotic breakdown is high.

The protest movement that began on 19 December has already notched an impressive achievement in compelling Bashir’s ouster. The peaceful campaign has drawn participants from nearly every stratum of society. Women have been prominent throughout. The urban middle classes have joined with farmers and herders to stage near-daily protests not just in the capital but also in smaller cities and rural villages. Traders, students and a cross-section of professionals, notably doctors, have all backed the campaign. Ruling-party supporters, including in the regime’s traditional strongholds, joined opposition activists in the marches. At the four-day, 24-hour sit-in outside the military headquarters that tipped the scales against Bashir, Sudan’s tapestry of religious and ethnic diversity was on vivid display, with members of Sufi orders mingling with Christians and singing together late into the night. Thousands of protesters have paid a high price, including imprisonment, torture and death, for their participation.

A number of factors explain the protesters’ impressive staying power and the authorities’ eventual decision to respond – up to a point – to the calls for change. First, discontent is widespread over the country’s economic crisis, which entails runaway inflation, crippling shortages of essentials including fuel and a currency crunch. All but the wealthiest Sudanese have felt the pinch. The government’s ill-judged attempt to increase the price of staples such as bread sparked the initial street actions that soon became a popular uprising. Secondly, many young Sudanese view their elderly leaders as representing a self-dealing, kleptocratic order focused on its own survival and unresponsive to their needs and aspirations. Thirdly, the security forces have themselves fractured, with mid- and lower-ranking soldiers joining with the protesters, making clear that the regime’s base has spindly legs. Ibn Auf reportedly delayed the announcement of a transitional military council for hours because many younger military officers were demanding a full handover to civilian hands. Bashir’s senior security sector allies had to intervene. Reportedly, the intervention was eventually announced after Ibn Auf, intelligence chief Salah Abdallah Gosh and head of the Rapid Support Forces militia Mohamed “Hemeti” Hamdan Daglo stitched together a backroom agreement to push Bashir aside.

Protesters are right to be sceptical of the ruling elite’s intentions. Ibn Auf, who will head the transitional military council, hardly represents a break with the past. He is one of Bashir’s most trusted confidantes, having been in his circle since 1989. He is allegedly complicit in some of the worst abuses in Darfur, where the regime’s scorched-earth campaign against rebels beginning in 2003 left between 200,000 and 300,000 people dead and 2.7 million displaced. The U.S. State Department placed Ibn Auf, who was head of military intelligence at the time, on a sanctions list in 2007. Some in the protest movement accordingly perceive the announced change as a game of musical chairs. As one protester told reporters in Khartoum, in a refrain that has repeatedly been voiced among the crowds: “They just replaced one thief with another”. Nor is it lost on many Sudanese that Bashir’s camp has played this game before. In 1989, when Bashir took power in a bloodless coup, he claimed to have detained one of his closest advisers, the National Islamic Front leader Hassan Turabi, in what was later revealed as an effort to disguise the putsch’s Islamist nature.

As Crisis Group has stressed since the protests broke out, many risks attend a political transition in a critical country in one of Africa’s more conflict-scarred neighbourhoods. To preserve his grip on power, Bashir kept the security forces fragmented. The danger of fighting among disparate armed groups in the event of a chaotic breakdown is high. Already, there are credible reports of clashes between elements of the army, who are more sympathetic to the protesters, and the loyalist National Intelligence Security Services. To smooth the transition, several steps will be required:

  • A first priority is to prevent further violence. Since December, security forces have repeatedly fired on protesters, killing dozens. In announcing Bashir’s ouster, Ibn Auf declared a 10pm to 4am curfew. In effect, he was ordering the thousands of protesters outside the military headquarters to go home. Sudanese authorities must not attempt to disperse the demonstrators by force. Such a move would be not only bloody but counterproductive. A lesson from the last four months is that repression – including Bashir’s 22 February order banning public gatherings and opening the door for mass roundups of protesters – has done little to change the course of the protest movement. Authorities should avoid violence and instead seek to reach an accommodation with protest leaders on the way forward.
  • More broadly, Sudan’s generals should rethink their outlined plan to rule by extra-constitutional fiat for two years. An African Union declaration adopted in 2000 expressly forbids military coups as unconstitutional changes of government. Unless the security forces quickly hand over power to a civilian-led transitional authority, the AU should suspend Sudan’s membership and follow up with sanctions. The leadership of the country’s security organs should see a clear self-interest in avoiding such ostracism by giving the reins to civilians. If they do not, protests will continue, raising the spectre of an ugly confrontation that could plunge the country into the deeper turmoil they say they are intent on averting.
  • Demonstrators should form an umbrella group and put its leaders forward to negotiate with the military council. Up to this point, protesters have been understandably unwilling to reveal their leaders’ identities given the security forces’ brutal record; they arrested and reportedly tortured the Sudanese Professionals Association leaders who issued public statements in January. With the transition having picked up pace, they should now change tack.
  • Ensuing talks should lead to a transitional authority along the lines Crisis Group has advocated since 2012: civilian leadership that includes members of the opposition, the ruling party and civil society; a defined period of constitutional reforms; and, at the end, free and fair elections. Without such a transition, Sudan should not receive the assistance from international financial institutions that it desperately needs to emerge from its economic doldrums.

International actors, viewed by protest leaders as having been lamentably quiet as campaigners braved police bullets, torture and arrests, need to weigh in more vocally and forcefully to achieve these goals and do everything possible to ensure protest leaders that do identify themselves come to no harm. The U.S. and EU, which both maintain ties with elements of the administration in Khartoum, should clearly warn against a violent crackdown and signal that individual commanders will face sanctions should they allow it. They should make clear that economic and other forms of cooperation with Sudan depend on genuine transfer of power to a civilian leadership. In a statement hours before the coup was announced, the U.S., UK and Norwegian governments called for an “inclusive dialogue” and asked Sudanese authorities to respond to protesters’ demands in a serious and credible way. They and others, including the EU, should follow that public message with behind-the-scenes diplomacy with the generals now in charge in Khartoum. Their message should be that greater repression will carry the price of continued isolation and will prevent Sudan from addressing the long-term economic and political crises underpinning the unrest. Sudan’s other partners, notably Qatar, Saudi Arabia, Turkey and the United Arab Emirates, likewise should encourage the military leadership to avoid a crackdown that would provoke further unrest and instability.

Sudan’s partners ought to move quickly to persuade military authorities in Khartoum to heed the Sudanese people’s call and allow for a credible, inclusive, broad-based transition.

Sudan sits at a strategic corner of Africa, surrounded by neighbours facing internal difficulties of their own. Not least of these is South Sudan, for whose peace agreement Sudan remains an important guarantor. Other adjacent states – Egypt, Libya, Chad, the Central African Republic, Ethiopia and Eritrea – will also watch developments anxiously. Should Sudan descend into chaos, the turmoil could spill across borders. Sudan’s partners ought to move quickly to persuade military authorities in Khartoum to heed the Sudanese people’s call and allow for a credible, inclusive, broad-based transition to steer Sudan to greater stability after Bashir’s long, chequered and bloody tenure.