MALAKAL, South Sudan – The dead were being counted in South Sudan’s capital on Thursday, after U.N. bases fell under fire and swaths of the city turned into an urban battlefield. The civil war, it appeared, had returned to the capital.
Even though the fighting had mostly stopped by Tuesday, many of the 45,000 people who fled the clashes searched for food and water, often without success. The United Nations had reached a critical shortage of basic aid supplies, officials said. Fear of continued fighting left markets bare and provisions scarce.
In the wake of yet another violent collapse of the world’s youngest country, the fate of the government and the international humanitarian mission here were thrown into question.
Just months ago, the country’s most prominent leaders, President Salva Kiir and Vice President Riek Machar, signed a peace deal that was meant to put an end to more than two years of fighting between their respective forces. It fell apart last Friday when their soldiers shot at each other outside the presidential palace, where both Kiir and Machar had come for a news conference.

That clash sparked a larger battle that left nearly 300 dead, according to government figures, including 33 civilians. But U.N. officials and aid groups said they believed the death toll was higher.
Zlatko Gegic, Oxfam’s South Sudan country director, said in an interview from Nairobi that he had seen photos of bodies piled on the streets of Juba, and doubted the official death toll.
“I hope the number will not reach 1,000 or more, but we may never know,” he said. “Relatives are collecting the bodies and burying them before they can be counted.”
The rift between Kiir and Machar’s groups is deep, driven by the country’s sometimes vicious ethnic politics, as well as a fight for access to the government coffers, including hundreds of millions of dollars in foreign assistance.
Few expected the peace deal to hold, but the recent schism nonetheless stunned the city because of the shocking level of violence and lack of concern for civilian lives or United Nations facilities. There are around 13,000 peacekeepers stationed in South Sudan, and many civilians have sought refuge on U.N. bases.
“The question of the day is whether Kiir and Machar have the ability to prevent a return to large-scale conflict,” said Gegic, who was evacuated this week along with other foreigners based in Juba. “Leer, Machar’s hometown, is said to be burning, and fighting is ongoing in Equatoria. The future is very hard to predict for us.”
What is predictable, to an extent, is the weather. South Sudan is currently in its wet season, which should last for another two months. The rains render large-scale troop movement difficult, analysts say, as the rough track roads that cross the riverine country become muddy and impassable. That means fighting in the near future will likely be limited to cities.
Last weekend, two major U.N. bases in Juba were struck by heavy weapons and small arms fire, even as thousands of civilians were running toward them for safety. U.N. officials asked repeatedly for the fighters to respect the international laws that protect their sites and personnel, but the calls were ignored. At least two Chinese peacekeepers were reported killed.
“They sacrificed their life in order to protect the world peace and regional peace,” the Chinese ambassador to neighboring Uganda, Zhao Yali, told the Associated Press.

“It is unclear now what further progress can be made under current conditions,” said Hervé Ladsous, the U.N. undersecretary-general for peacekeeping operations in a news conference in New York on Wednesday.
Government leaders from Kiir’s side claimed that the United Nations was knowingly harboring opposition fighters and said that was one of the reasons the compounds were struck.
“The U.N. will say what it wants, but it knows that there are [opposition] fighters there,” said Martin Lomuro, South Sudan’s minister of cabinet affairs, in a telephone interview on Thursday. The United Nations denies taking sides in the conflict.
South Sudan became independent from Sudan almost exactly five years ago, after a referendum that was lauded by the international community, even as signs of internal fractures emerged in the country’s leadership. In late 2013, the country exploded into civil war that took on ethnic overtones between the Dinka tribe, which Kiir belongs to, and the Nuer, Machar’s tribe.
Tens of thousands were killed.
I hope the number will not reach 1,000 or more, but we may never know
While both Kiir and Machar have said they still back the peace process, many here are worried that cycle of violence could repeat itself, with battles spreading outside the capital.
In recent days there has been fighting in Leer, a small city in northern Unity State. Fighting also escalated in Eastern Equatoria state, and aid groups were forced to suspend their work there. Though those clashes appeared to be limited, other cities across the country waited nervously as rumors swirled that Machar’s men were moving north. Aid groups continued to evacuate employees from the country. The United States sent 47 troops to help protect the American Embassy in Juba.
In parts of the country, the tension between factions is grounded in local feuds, often over land rights. The town of Malakal, for example, changed hands roughly a dozen times during the course of the civil war and is now controlled by Dinkas. But leaders of a third ethnic group, the Shilluk, who are loosely aligned with Machar’s Nuer forces, have vowed to take it back.
The U.S. government played an integral role in the country’s creation, and has been at the center of post-independence peace negotiations. The U.S. government is the largest provider of aid to South Sudan, and Riek Machar’s wife is an American citizen, both of which give the United States extra leverage if it decides to impose new sanctions. But some analysts say that U.S. officials have failed to realize the intensity of the hostility between the country’s leaders.

“Having worked so closely with Kiir and Machar in achieving independence, U.S. officials have been reluctant to acknowledge that their proteges haven’t lived up to expectations,” said J. Peter Pham, the director of the Atlantic Council’s Africa Center. “The U.S. engaged in a bit of wishful thinking: they arranged a shotgun marriage between two men with a history of animosity towards each other.”
Several months ago, the United Nations brokered an agreement allowing 1,300 of Machar’s troops back to Juba, which was seen as a move toward peace. But it was that same force that participated in the week’s fighting. South Sudanese officials on both sides of the divide have said that the agreement that mandated that both forces have a presence in Juba only made the city a tinder keg.
“You can’t unite two forces that have no trust, that do not share commands,” said Deng Dau, a member of parliament. “The agreement created many unresolved issues.”
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