The United States ordered the departure of diplomatic personnel from Juba, South Sudan’s capital, over the weekend, and Uganda dispatched special forces to the city, just as it did at the start of South Sudan’s last civil war in 2013.

The actions of both governments suggest that they think there is a credible risk of violence erupting in the capital.

International Crisis Group, a think tank that works to prevent and analyze conflicts, issued a warning March 7th, saying, “South Sudan is on the precipice of full-blown war.” It linked the brewing crisis to the ongoing war in neighbouring Sudan, saying, “The precarious national détente [in South Sudan] is now under threat, thanks in no small part to the civil war raging in neighbouring Sudan.”

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Conflict is already raging in (north) Sudan, Somalia, Mali, Niger, Burkina Faso, and in the Democratic Republic of Congo. There is also a risk of renewed war between Eritrea and Ethiopia, and within Ethiopia. These conflicts threaten a regional conflagration not seen since the late Cold War and the Soviet collapse, which destabilized a number of regimes in Africa.

During the Second Sudanese Civil War (1983-2005), Africa’s longest modern war, several regional powers intervened, including Uganda, Ethiopia, Eritrea, and Iran. The war resulted in a fragile peace from 2005 to 2011, culminating in the breakup of Sudan and South Sudan in 2011. Soon thereafter, South Sudan fell back into war, as the former rebel army (SPLA, now called SSPDF), unaccustomed to governing, split into two camps and battled for the spoils of statehood. That war lasted from 2013-2018, with occasional sub-national fighting continuing thereafter.

Fortunately, South Sudan was largely spared when the Republic of Sudan fell into its own civil war in 2023, which ravaged the capital and other cities—something that had never happened in any of Sudan’s previous wars since independence in 1956, which were largely contained to rural peripheral parts of the country.

Although spared direct violence, South Sudan suffered economically. The war cut off an oil pipeline that South Sudan relied on for two-thirds of its state revenues, plunging the country into a fiscal crisis. Disgruntled soldiers and civil servants have now gone unpaid for months, or even years in some cases. Adding to the economic pain, the largest development and humanitarian donor in South Sudan, the United States, has abruptly cut back funding as the new Trump Administration has reduced the size and budget of USAID, the US Agency for International Development.

International Crisis Group, in its briefing, noted that South Sudan’s economic woes have “deprived the president of the funds that sustained his patronage network, straining his ability to keep his regime afloat. Discontent is widespread.”

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Former opposition fighters throughout the country, who were supposed to be demobilized, disarmed, or integrated into the South Sudanese military (SSPDF) under the terms of the 2018 peace agreement, remain independent and armed.

Fighting erupted last week in Nasir, a long-time opposition stronghold near the Ethiopian border, between SSPDF troops and the ‘White Army,’ a Nuer militia tied to the opposition SPLM-IO, though not necessarily directly controlled by it. During this fighting, a South Sudanese army base was overrun and a battalion of troops was killed or scattered. The fighting may have been triggered by fears that SSPDF intended to disarm the local militia.

A UN helicopter crew member was killed while attempting to evacuate South Sudanese army troops from Nasir, when Nuer militia fighters opened fire on them.

Subsequently, security agents in Juba arrested high-profile officials belonging to the SPLM-IO, which is the minority party in government, as well as military officers affiliated with SPLM-IO, most of whom belong to the Nuer ethnic minority.

International Crisis Group says that these arrests threaten the fragile unity government, formed under the 2018 peace deal: “Tension in the capital Juba is sky-high…. More combat in Upper Nile is likely. From there, it risks merging with the war in Sudan, potentially triggering prolonged proxy fighting in South Sudan.”

Malual Bol Kiir, a South Sudanese peace advocate, offered a more measured assessment, writing, “While the clashes in Nasir may not immediately derail the peace process, they represent a serious warning sign. South Sudan is at a critical juncture where unresolved security challenges, political instability, and economic hardships could converge to reignite widespread conflict… The Nasir incident has already shifted the political and security landscape, raising fears that similar clashes could erupt in other parts of the country where tensions remain high.”

Malual called for urgent action by the African Union, Intergovernmental Authority on Development (IGAD), and the United Nations (UN), which played a role in brokering the 2018 peace agreement. IGAD’s Secretariat has scheduled an extraordinary summit of heads of state, to be convened virtually later today.

Nicholas Haysom, Head of the United Nations Mission in South Sudan (UNMISS), spoke with Al Jazeera on Monday about the political crisis. He was asked how close the country is to war. He replied, “That is a principal concern. A relapse back into conflict would be catastrophic. It would certainly be reminiscent of the civil war they had after their independence in 2011, and it would also overload the region, which has enough wars ravaging it as we speak.”

Haysom said both President Kiir’s faction, the SPLM, and Vice President Machar’s faction, SPLM-IO, are responsible for the escalation of tensions in the country.

Uganda backs ailing South Sudanese president

In a series of posts on social media over the past two days, Uganda’s military chief, Muhoozi Kainerugaba, who is also the son of President Yoweri Museveni, announced the deployment of troops to Juba, and vowed to back South Sudan’s ailing strongman, President Salva Kiir, in a potential war with the armed opposition.

“We the UPDF [Uganda People’s Defense Forces], only recognize ONE President of South Sudan, H.E. Salva Kiir, he is our 'Afande' [Swahili military title] even in UPDF because he is the younger brother of Mzee [President Museveni]! Any move against him is a declaration of war against Uganda! All those who commit that crime will learn what it means!” Muhoozi, a frenetic and combative user of X, formerly Twitter, added, “We shall protect the entire territory of South Sudan like it was our own. That is the will of the Commander-in-Chief!”

Muhoozi also posted a video of UPDF soldiers disembarking from an aircraft. Sudan War Monitor geolocated this video to the Juba International Airport and identified the aircraft as an A-320 belonging to Freedom Airline Express, a Somali-Kenyan airline that operates both charter flights and fixed routes, mostly to destinations in Somalia.

Data from a flight tracking service indicates that this aircraft made at least one flight from Nakasongola Airforce Base in Uganda on Tuesday, March 11, and arrived in Juba the same day. Additional forces may have arrived earlier. According to the the Ugandan army chief, the deployment into Juba began March 8, the same day that the U.S. ordered its diplomats to leave South Sudan.

Witnesses and additional video clips indicate the movement of UPDF troops through Juba streets, though their final destination and the size of the contingent is unclear.

In response to this development, South Sudanese opposition activists spread rumors that Kiir’s government is paying Ugandan soldiers as much as USD 200 per day, even as South Sudanese soldiers go unpaid. “Our primitive soldiers can't show their anger because tribalism and sycophancy are holding them back,” wrote one critic on X.

For background, the start of the last South Sudanese civil war began in 2013 began with an orchestrated massacre of Nuer in Juba by forces loyal to President Salva Kiir. Hundreds of thousands of Nuer subsequently fled into UN-run ‘protection of civilian sites,’ as well as into exile as refugees in neighboring countries. Opposition forces retaliated, perpetrating war crimes of their own, including in the cities of Bor, Malakal, and elsewhere, where they overran army forces.

Uganda’s government backed Kiir’s government immediately, deploying troops to protect the capital and drive the opposition out of Bor. From 2013-2015, Uganda stationed troops in Juba, Bor, and along the Nimule-Juba highway, helping to stabilize Kiir’s government, which ultimately emerged as the winner of that war.

Speaking on a television program yesterday, Nyagoah Tut Pur, a researcher at Human Rights Watch, noted that the former civil war in South Sudan resulted in “horrendous, horrific crimes,” for which there was generally no accountability. “At Human Rights Watch, we have been advocating for the establishment of a hybrid court that would investigate and try individuals who are responsible for the most serious abuses.”

Succession struggle 

South Sudan has not held elections since its independence in 2011 and the country’s leader is visibly frail and rumored to be seriously ill. Despite this, Kiir appears unlikely to step down. “The political jockeying in Juba is no longer about elections, it’s more about President Kiir and his succession,” said Alan Boswell, International Crisis Group’s Project Director for the Horn of Africa, speaking on Al Jazeera.

“I think the general view is that there will probably not be elections, or at least Kiir will probably not step down while he is still alive. So a lot of the jockeying now among the South Sudanese political elite is basically about what happens when President Kiir is no longer around, essentially, and what that means for [Vice President] Riek Machar.”

He added, however, the conflict is not just about individuals:

“We talk about these two men but they both hold together respective political coalitions, and even when they’re gone, South Sudan is likely to still face many of the problems unless they can sit down and essentially do what they should have done before independence, which is sit down and have a proper national discussion about what power in the country looks like, how they will structure the country, how oil revenue will be spent, etc. They just didn’t do that before their independence, and no one made them.”

UAE strengthens ties with South Sudan 

Throughout most of South Sudan’s independence, the two Sudans have enjoyed mostly peaceful relations, apart from a brief but intense border war in 2012, and some Sudanese weapons deliveries to opposition groups during the 2013-2018 civil war.

The two countries have depended on each other economically, and they also cooperated on security matters as they each struggled to quash internal rebellions. Last year, for example, SAF coordinated with South Sudanese authorities to arrest SPLM-IO commanders suspected of recruiting mercenaries on behalf of the RSF.

Sudan’s military ruler, Abdel Fattah al-Burhan, has visited Juba several times since taking power in a coup in 2021, and he tried to keep positive relations with his South Sudanese counterpart. Most recently, he visited Juba in September last year to discuss economic and military matters, as his government struggled to contain the RSF rebellion. After this meeting, SAF secured the help of South Sudan in repatriating soldiers that had fled across the international border to avoid capture by the RSF.

However, relations have deteriorated more recently, as Kiir has struggled to maintain neutrality in the face of pressure from both SAF and RSF, and following a massacre of South Sudanese civilians in Wad Madani, Sudan, which triggered nationalist sentiment in South Sudan and a wave of reprisal attacks against Sudanese merchants in markets throughout the South.

Meanwhile, Kiir appears to have grown increasingly paranoid and erratic, sacking, appointing, and reshuffling cabinet members at a frenetic pace, as well as generals, governors and other officials. Kiir’s growing political isolation and fiscal desperation could be pushing him closer to the United Arab Emirates, which is widely viewed as being the principal patron of the RSF, the insurgent paramilitary fighting Sudan’s army.

International Crisis Group noted in its briefing,

“Kiir alienated several of his most prominent allies through a firing spree that started with his long-serving intelligence chief, Akol Koor, in late 2024 and culminated in the sacking of two of his vice presidents – a move that politicians in Juba interpreted as positioning his adviser and moneyman Benjamin Bol Mel, whom he appointed as one of the new vice presidents, to be his successor. Bol Mel was one of Kiir’s principal negotiators with the RSF and has recently spent significant time in the UAE.”

“The president is facing other challenges besides. Rumours are rampant that Kiir’s health is failing, which has intensified the jockeying over the presidential succession. As noted, Kiir does not appear to have the cash he used to help paper over such divisions as in the past.”

Last week, the UAE inaugurated a charitable project in South Sudan, the 100-bed Madhol Field Hospital, similar to a hospital in Amdjarass, in Chad, which The New York Times exposed as being a cover for a drone base and weapons smuggling to the RSF. Like the hospital in Chad, the UAE’s new hospital in South Sudan is very close to the Sudanese border, located in Aweil East, bordering RSF territory.

This development has provoked the Sudanese military, straining relations.

South Sudan’s Foreign Minister Ramadan Abdallah Goc denied that the hospital was related to any UAE effort to undermine Sudan, saying the border location was chosen because Northern Bahr al-Ghazal was in dire need of medical services.

Another source of tension is the recent political alignment of the SPLM-North with the RSF. The SPLM-North, a Sudanese rebel group that controls the Nuba Mountains, historically has close ties with Kiir’s government and the South Sudanese ruling party. Both were part of the original rebel movement (SPLM) that fought the Sudanese government during the Second Sudanese Civil War.

Although the SPLM-North has not made a formal military pact with the RSF, it is increasingly demonized in Sudanese state media and in the pro-SAF military media, signaling the likelihood of escalation in the Nuba Mountains. Recent SAF gains in North Kordofan bring the military closer to relieving the sieges of Dilling and Kadugli, garrison towns in the Nuba Mountains cut off by SPLM-N the RSF. 

Overall, the local and regional alignments in Sudan and South Sudan are complex and nuanced. The two countries have a combined population of about 65 million, which is 2.5 times the population of Syria, or nearly the population of France. The risk of state collapse in one or both of these countries, which is real and growing, threatens to send millions of refugees into neighboring countries and beyond. Moreover, the conflict could spill over into parts of Chad and the Central African Republic. The human toll of such a regional conflict would be immense.

However, this scenario can be averted. Kenya’s President William Ruto is among those who intervened recently, calling both Kiir and Machar on March 6 to speak about the escalating security situation in the country. “I implored both leaders to engage in dialogue toward fostering peace in the country,” he said in a statement afterwards.

International Crisis Group says that South African President Cyril Ramaphosa and Ethiopian Prime Minister Abiy Ahmed, as well as the UN peacekeeping mission Sudan, are potential interlocutors who could help deescalate the situation. At the same time, Crisis Group says that UNMISS needs to be ready to act to “help prevent massacres along ethnic lines (as occurred in Juba and elsewhere in 2013), including by sheltering any who may flee to its bases should violence erupt and by preparing mobile units that can respond quickly to protect civilians trapped by fighting.”

“Though South Sudan could quickly slip back into full-scale conflict and ethnic bloodletting, such horror may still be averted if regional leaders intervene with high-level diplomacy before the situation spins further out of control.” Source: Sudan War Monitor