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The war in Equatoria

A rare look inside South Sudan's spreading conflict

Jason Patinkin/IRIN
SPLA-IO soldiers ride on the back of a pick up truck through a rebel-held part of South Sudan's Kajo Keji county

When South Sudan’s civil war broke out in 2013, much of Equatoria – the country’s breadbasket ­– managed to stay out of the conflict. But that respite was short lived. As the government army began purging the region of perceived opponents last year, it triggered the world’s fastest-growing refugee crisis, with the United Nations warning of a potential genocide.

Reporter Jason Patinkin and videographer Simona Foltyn travelled to rebel-held Equatoria and the refugee camps across the border in northern Uganda to report on the human cost of South Sudan’s brutal civil war. This is what they found.

Pastor Cosmas Lodiong crouches over a dark stain on a concrete walkway in Jalimo, a small town in the forested hills of Kajo Keji county in South Sudan's Equatoria region.

"Someone was killed here," he says. "He was a civilian. He was a peasant."

Two weeks earlier, in mid-April, government soldiers from a garrison to the south stormed Jalimo after clashing with rebels, the pastor says. In total, they killed four people in the town, all civilians, before setting fire to dozens of homes. The "peasant" was named Joseph Duku, according to Lodiong.

The other three deceased had been drinking tea down the street when soldiers pulled them from their chairs and shot them dead. Lodiong was outside the town at the time of the killings and ventured to Jalimo once the gunshots stopped. Duku's relatives buried his body. Lodiong placed the rest in a mass grave on the edge of town.

Like most of South Sudan, Kajo Keji is at war. In towns like Jalimo, bullet holes mark the walls of stores, shell casings litter the roadways, and dozens of homes are burned black. Rebels occupy the town, in view of a government garrison across a green valley. Nearly all the civilians have fled to Uganda, with the few who remain plagued by hunger, disease, and fear of the next battle.

Although he is Jalimo's pastor, Lodiong himself no longer lives here. He only came to show IRIN the mass grave. If Jalimo is any indication, South Sudan's war, now in its fourth year, shows no signs of stopping.

"I pray that God listens to the pastors so peace comes," says Lodiong.

Equatoria explodes

Kajo Keji has a long history of conflict. A half century ago, when Sudan was still united, southern Anyanya rebels held bases in the county during the country's first civil war, which lasted until 1972.

When southerners again rebelled in the 1980s and 90s, Kajo Keji served as a rebel headquarters for the SPLA, the rebel outfit that is now the name of the independent nation's government army. When the Second Sudanese Civil War ended in 2005, Kajo Keji at last enjoyed peace, earning a reputation for its fertile fields and well-educated populace.

Even after the latest civil war broke out in 2013 – mostly pitting ethnic Nuer rebels of former vice president Riek Machar against the largely Dinka army under President Salva Kiir – Kajo Keji, like much of Equatoria, managed to remain at peace and stayed out of the conflict, which devastated the country's northeast.

Ironically, it was a peace deal between Kiir and Machar that marked the return to large-scale violence in Equatoria, which covers the country's southern third.

In August 2015, the two men signed an agreement making Machar the country's First Vice President. The deal also gave both the government and rebels the right to establish bases around the country to canton their troops.

For Machar's side, called the SPLA-In Opposition, or simply "IO", these "cantonment sites" presented an opportunity to grow his army in Equatoria, and the rebels heavily recruited soldiers to fill any allotted bases.

Jason Patinkin/IRIN
A rebel soldier walks with his weapon in Loopo, near the frontlines in South Sudan's Kajo Keji county

To curtail the recruitment, the government deployed its most notorious militia to Equatoria, called the Mathiang Anyoor. Comprising young Dinka recruits, the Mathiang Anyoor counter-insurgency strategy had little to do with winning hearts and minds.

Instead, according to interviews with dozens of Kajo Keji residents, the Mathiang Anyoor carried out a campaign of terror against the local population – arresting, disappearing, or even killing anyone with suspected links to the IO.

"They torture with an intention of you telling them where the IOs are, and we even don’t know where the IOs are," said Mary Yawa, a woman from Gaderu village in rural Kajo Keji, speaking from Uganda where she is a refugee.

Such abuses exacerbated the longstanding ethnic divide between the Equatorian population, who are mostly farmers, and the livestock-rearing Dinka from other parts of South Sudan.

"Those Dinkas, since they came, we knew they had bad intentions," said Yawa, who like many Kajo Keji people refer to the government primarily in ethnic terms.

In July 2016, the peace deal fell apart. Machar's and Kiir's forces, both stationed in the capital Juba, fought each other for days, before Machar fled the city with his men, eventually escaping to the Democratic Republic of Congo.

Equatorian militia who had joined him broke off to raise rebellion, engulfing the region in violence.

In Yei and Lainya, areas to the southwest of Juba, Dinka troops slaughtered Equatorian inhabitants in their attempt to subdue the rebels. At the same time, Equatorian militia killed Dinka civilians living in the region. Hundreds of thousands of refugees poured into Uganda and Congo, creating the largest human exodus in Africa since Rwanda's 1994 genocide. By the end of 2016, the United Nations said ethnic cleansing was underway and warned of genocide.

Kajo Keji managed to avoid the worst of this violence throughout last year. The IO's commander in the county, a former police officer named Moses Lokujo, led only a small outfit of insurgents based in forest camps in two of Kajo Keji's five payams (administrative districts).

But abuses of civilians continued. "Boso, Kenyi, Soro, Yoku," recalled Yawa, listing the names of men taken in her town. "We believe they have been killed because some were arrested in August and until now we have never seen them."

By November, she fled to Uganda. Within two months, nearly all of Kajo Keji's residents had joined her.

'Whose parents will be killed?'

Emmanuel Murye had just been ordained as the new Episcopal Bishop for Kajo Keji when the county descended into war.

On 20 January, according to Murye, the rebels assassinated Oliver Jole, a well-known civilian official in Liwolo town in the county's west, accusing him of being a government collaborator. Over the next week, the IO attacked government forces near Mondikolok in the northeast, and hijacked a vehicle on the road to Juba. In response, government forces mobilised and clashed along the Juba road with the rebels, who then withdrew to the forests.

After the battle, according to Murye, the government forces returned to Mondikolok, turning their guns on the civilians and killing five including a religious teacher, an elderly disabled man, a passed-out drunk with bullets sprayed into his back, and a woman who the soldiers raped, shot in the vagina, and set on fire. They also killed a sixth person, a member of the IO.

"That was very terrifying to the people of Kajo Keji," said Murye, who oversaw the burial of those killed at Mondikolok. "They are saying six people were killed, and now you start to fear: Who will be the seventh? Whose child, whose parent will be killed?"

Kajo Keji quickly emptied. Even Murye left, piling furniture, books, and files into trucks and relocating his entire diocese to Uganda.

This mass depopulation inadvertently benefited the rebels. Without civilians, towns had no functioning markets, leaving the government with few supplies and little ability to extend its reach beyond its garrisons. But the rebels, who had already survived in the bush for months or years, could fill the empty countryside.

The next month was chaos. Clashes erupted in Lire, Kajo Keji town, Loopo, Jalimo, and at Jale and Bamure near the Ugandan border.

See our map on the control of key towns and details of human rights abuses. Hover on each incident to learn more:

For the rebels, the turning point was at Jokat, a forest hamlet on the main road linking Kajo Keji town to the west of the county where they ambushed a government convoy, killing soldiers, taking weapons, and stealing vehicles. Since then, the government has never penetrated any further west. The government still holds four garrisons in the east, but the rebels roam the rest.

In what is effectively a bloody stalemate, the rebels lay ambushes on government convoys along the roadways, confining the SPLA's permanent presence to its garrisons. But the rebels are also unable to fully protect their areas. Two weeks before IRIN's visit, after clashing with rebel forces who withdrew to the bush, government forces ransacked the town of Loopo and rampaged through Jalimo before returning to their bases unscathed. When the fighting stopped and the dead were buried, the front lines had not changed.

Still, such a situation counts as a relative success for the rebels. In the last year, faced with better equipped government forces, they've lost key towns in Unity, Upper Nile, and Jonglei states in the northeast. Machar himself sits under house arrest in South Africa. But in Kajo Keji, the rebels have gained ground, with a presence now in all five payams of the county.

Part of the rebels' success is their improved organisation in Equatoria. What started as a collection of local self-defence militias has come to resemble a more integrated fighting force.

Lokujo's unit comprises troops from across Central Equatoria, as well as Nuer fighters who moved south with the war. They have radio communications with rebels in other states, and during IRIN's visit Lokujo coordinated operations with troops in Eastern Equatoria. A specialised intelligence unit moves around the area, sometimes crossing between South Sudan and Uganda (Lokujo did not allow IRIN to interview or photograph members of this unit).

Equatorian Front, South Sudan

Another key to the rebels' gains is their support among Kajo Keji's civilians. In Logo IDP camp in the west of the county, Agnes Kiden, a mother of seven, said she felt safer with the rebels in control.

Kiden fled to Logo after men she said were Dinka soldiers killed her husband and three-year-old daughter, before raping and killing her sister-in-law. "The IO boys, they are the ones helping us for now, because when I compare what they do with what the government used to do, it's a big difference," she said in an interview inside her hut of sticks and plastic sheeting.

"The government forces could kill, rape, steal, a lot of atrocities, but these ones [of IO], I can sleep even in a place like this one and nobody can come."

With this acceptance comes food for the IO. Some wealthier local businessman buy it in bulk for the rebels, including a lorry-full of grain trucked in from Uganda during IRIN's visit. But the insurgents mostly rely on smaller donations from regular civilians. Civilians said they were willing to share their food with the rebels simply because the IO asked them nicely, whereas government soldiers demanded it or just took it by force.

However, the rebels do lack one key resource: weapons. The international community has refused to impose an arms embargo on South Sudan as a nation, which would be designed to block weapons to the government and rebels alike. Instead, regional governments and the West have acted in concert to prevent weapons flows to the rebels only.

Earlier in the war, Machar's side received a trickle of arms from the government of Sudan, but this has since been blocked by the United States, which in turn has promised sanctions relief to the Sudanese government of Omar al-Bashir, partly in exchange for cutting off the trade.

Uganda has also effectively prevented any weapons from flowing through its long border with South Sudan to the rebels, though numerous UN reports accuse Kampala of providing weapons to Kiir's government. That leaves the rebels in Equatoria with only the guns they took with them when they defected, or which they steal on the battlefield, a point of pride among soldiers.

"They are buying for us," Lokujo joked about the government's arms purchases. "Instead of making development, they are using our resources to buy weapons. So, these weapons, we have the right to use them."

Jason Patinkin/IRIN
Moses Lokujo speaks in Loopo surrounded by his troops

Lokujo's confidence belies the gravity of their lack of arms. The rebels have so little ammunition that, under Lokujo's orders, any soldier who wastes bullets receives a lashing across the back. The rebels' inability to defend Loopo and Jalimo in mid-April, when government troops burned homes and shot civilians, is further proof that they are outgunned and cannot adequately protect civilians.

Interviews with dozens of Kajo Keji residents, both inside and outside the county, describe atrocities in Kajo Keji that indicate a pattern of collective punishment: After fighting with rebels, government forces target civilians who they accuse of being linked to the IO.

IRIN can report 22 civilians killed by the SPLA in Kajo Keji in 2016 and 2017. This compared to one – the assassination of Oliver Jole – by the rebels in the county.

But the seeming predictability of government retribution on civilians after IO attacks raises questions about the culpability of the under-equipped rebels, who are willing to attack the government forces despite knowing it is non-combatants who will bear the brunt afterwards.

"Sometimes the IO do a small attack on the government, then run away," said one refugee in Uganda who did not want to use her name because she feared reprisals since her husband was in the IO. "Immediately, the soldiers don't find the IO, but they find the civilians, and they are the ones to suffer."

Civilians hanging on

Direct violence isn't the only threat to Kajo Keji's civilians. Taban Dafala is the only doctor in the clinic in Jalimo, the furthest east IRIN saw civilians in the county. With a stubbled face and tired eyes, he treats about 10 people per day, compared to 60 before the war, as so many have fled.

The town is home to the IO – Dafala and his assistant are the only civilian inhabitants. Dafala's patients do not live in Jalimo. Instead, they come in each day from the bush for treatment before returning to their forest hideouts.

"Malaria is the major problem, then typhoid, hook works, worms in general, fungal infection, skin problems," he said. "There is no water, even for bathing, for washing clothes, and that's why the skin diseases are affecting them."

Dafala doesn't have enough drugs to treat his patients. There's not even a first aid kit, he said. This lack of medicine and basic supplies is similar across the county because the government has largely blocked aid deliveries, including at least six convoys of aid sent from Juba for the displaced persons camps in the county's west. Government forces would not let them enter rebel areas.

The few drugs in Dafala's clinic are mostly painkillers and antibiotics that he bought with a donation from a foreign aid group and smuggled across the border on a motorbike, avoiding official border crossings manned by government troops.

"I am using the shortcuts," he said. "If I come by the government soldiers, I will be arrested, because when I transport drugs here, they may say I am coming to treat the IOs."

Jason Patinkin/IRIN
A family of displaced civilians share a meal next to their hut in Logo camp, where over 16,000 people have taken shelter in a rebel-held part of South Sudan's Kajo Keji county

The majority of the civilians still in Kajo Keji are in the three camps in the west, loose collections of mud, grass, and plastic huts. Collectively, they house around 30,000 people, according to the UN.

In Logo, a camp of some 17,000 near the Ugandan border, residents complain of hunger. A few aid groups have managed to slip across to deliver seeds for the people to plant, but there have been no general food distributions, and little else.

The problem is that even the aid coming from Uganda is controlled by Juba. Unlike in previous wars in Sudan, aid groups have refused to launch parallel operations from neighbouring countries to reach civilians in rebel areas.

That means anything brought in from Uganda is coordinated through aid agencies in Juba that operate with government permission. Juba-based aid workers who travelled to Logo on day trips from Uganda were so worried about Kiir’s government revoking their meagre access that they asked not be quoted, photographed, or have their organisations named.

"As long as it is humanitarian, it is to be respected, but if [the government] are not [respecting], then we better take humanitarian assistance from outside South Sudan to access people in need," said Francis Dabe, an IO relief official from Kajo Keji living in Uganda.

'Not fit for us to stay'

With ongoing conflict and little aid in Kajo Keji, some three quarters of the county's population have gone to Uganda, settling in sprawling camps that now house nearly one million people, most of whom have entered in the last year.

It is as if the entirety of northern Uganda west of the Nile has been converted into a vast camp. One can drive for hours across the region and remain amid the amorphous, sprawling collections of tents, their white plastic sheet roofs gleaming through the sparse forests.

Ugandan authorities are quick to point out that these are "settlements" rather than traditional camps, because they are interspersed with local Ugandan villages. It is all part of Uganda's open-door refugee policy, often held up as a model in a time when Western nations are taking steps to limit migration.

Humanitarian Blockade, South Sudan

But Uganda's principled policy has hardly translated into a good life for the refugees. Camp conditions are harsh. Water, trucked into the vast region, is in short supply, and medical clinics are rare.

Yawa, who lives in Bidi Bidi, the largest of the settlements, holds up her small son, whose skin is covered in a rash similar to the ailments afflicting people in Jalimo. "This place is not fit for us to stay in," she said.

Above all, the refugees complain of hunger. Aid groups originally supplied 14 kilograms of grain per month to each refugee, but this was cut to 12, and is now down to just six per month. From that ration, refugees like Yawa must sell some of the grain to pay for other basic items like soap.

Making matters worse is that the rations often don't arrive on time, forcing refugees to make dangerous, even deadly, decisions to find food. Earlier this year, after not receiving food for most of January and February, Yawa and 15 others in Bidi Bidi decided to make a risky return to Kajo Keji in hopes of harvesting the cassava fields they'd abandoned.

But upon reaching their village, they ran into government soldiers who opened fire, killing three, including Yawa's brother Victor Sokiri, a pastor. Fearing the soldiers' return, they buried the bodies in graves only a foot deep, and returned to Uganda for good.

"I will not go back again," Yawa said.

Jason Patinkin/IRIN
Seeds distributed in Logo refugee camp. Aid is blocked from South Sudan, so these came from Uganda

Part of the problem is that Uganda's open-door policy is based on providing basic services to local Ugandans in exchange for giving land to refugees. But faced with a funding shortfall of nearly $2 billion – as well as allegations of corruption among aid groups – there isn't enough aid for the refugees, much less the communities who accept them.

In one Ugandan village among the Bidi Bidi settlement, a group of elders complained to IRIN that while they welcome the South Sudanese, they have yet to see any tangible benefits from their government or aid groups.

"They didn't give us anything," said Haji Ramadan Almas, an imam. "They are supposed to dig boreholes and to build some schools."

Such disappointment can escalate into resentment as the two communities compete for resources, particularly firewood. In some cases, locals have even threatened refugees with violence as the refugee influx results in deforestation.

"They came with bows, arrows," refugee Betty Jagoro told IRIN, describing a party of locals who came to stop her and other refugees from collecting firewood near a Ugandan village. "We saw the way they are coming, the tactics. It did not look good, so we had to take off."

Meanwhile, ethnic divisions between refugees themselves have turned violent. In a twisted reversal of the situation in South Sudan, Equatorian refugees in Uganda have taken out their anger against Kiir's government on Dinka refugees, some of whom had previously been their neighbours in towns like Yei.

In December, an Equatorian mob reportedly beat a group of Dinka women at a food distribution point, accusing them of being the cause of their suffering.

In early June, Ugandan media reported that members of four Equatorian tribes ganged up on a group of Dinka in Lamwo district, injuring two who needed medical treatment, likewise accusing them of being at fault for South Sudan's conflict.

And, in yet another case, Equatorian refugees pulled an elderly Dinka man off a bus, slashed him across the face with knives, and robbed him, according to his sister, Rachel Kuang, who has lived in Uganda as a refugee since fleeing a separate conflict in South Sudan in 2012. The situation has become so bad that Ugandan authorities have started settling Dinka refugees separately from others to minimise violence.

"Before, there were no problems, the relations were good," Kuang said. "When the people started coming from Yei and Kaya, that's when the problems started coming."

Going underground

There is now an ever-present fear of the war itself entering Uganda. The IO accuses the South Sudanese government of transporting troops through Ugandan territory and of using it as a refuge after battlefield retreats.

In April, Uganda's military had to block South Sudanese government soldiers from entering Uganda to attack civilians fleeing a massacre in the town of Parjok, in Eastern Equatoria.

"It was the SPLA," said Apollo Kazungu, Uganda's refugee commissioner. "We had to tell them, 'Look here, these are refugees, please go back.' "

Since then, militants have succeeded in crossing the border. In the last month, gunmen in South Sudanese uniforms raided refugee encampments in northern Uganda, stealing cattle and attempting to abduct civilians.

Uganda's political involvement in South Sudan's war creates additional risks. Ugandan President Yoweri Museveni has played both sides of the conflict, sending troops and weapons to the government while assuring Equatorian IO officials that there is a safe haven on Ugandan soil.

This double game means both rebel and government agents operate in Uganda, creating potential for further violence. 

In 2015, suspected Kiir agents allegedly assassinated South Sudanese opposition figure Peter Sule and IO official Elias Lino Jada in northern Uganda.

In January of this year, Ugandan police arrested Dabe, the IO relief official, in Uganda's northern Moyo district. In Dabe's telling, the police accused him of smuggling weapons but refused to officially book him or take a statement. Dabe was later released thanks to intervention by higher level officials in the Ugandan government who have assured IO officials of safety.

Now, most IO members in the country are underground, and avoid places like Moyo.

"IO members [in Uganda] live in fear of arrest by the regime in Juba and abduction by individuals in Uganda community who might take bribe and abduct these members and hand them over to Juba," said one rebel official in Kampala, who declined to be named. "No one knows where my family lives. I do my business outside, but never bring anyone home."

Fifty more years

As the war worsens in South Sudan and puts more pressure on its neighbours, there seems little on the horizon that can bring an end to the conflict. The government has broken its own ceasefire, while the rebels fight on despite Machar's exile. No credible peace process exists.

Jason Patinkin/IRIN
Refugee camp in Uganda during the rains

Back in Kajo Keji, the rains have begun, which usually means a lessening of violence. But the IO see the change in weather as an opportunity. The dry season, after all, was a success, and the rains can give the guerrillas – less reliant on mechanisation – an advantage.

To Lokujo, there is no reason to stop fighting just yet.

"Of course more lives will [be lost in] South Sudan, so it's not easy. But a movement cannot be destroyed," he said. "Even more than 50 years we can stay here."

Kajo Keji has already experienced one half century of fighting. It's easy to see the latest conflict lasting just as long.


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