Even in a war of rapidly fluctuating military fortunes, Malakal stands out: the capital of Upper Nile state changed hands six times between December and March. And even in a war characterised by massive atrocities, Malakal has been hit particularly hard: the number of civilians killed by both sides may never be known, but it is clear that patients were shot in their hospital beds, among numerous other human rights violations.

Malakal is now a shrunken shadow of its former self, a distressing sight for anyone who knew the town before. Market stalls are shuttered, where the doors haven’t been bashed in, or burnt. Some abandoned residential areas, which bore the brunt of the fighting, are now over-run by foliage, the town returning to the bush; the UN estimates that 22% of the town was destroyed.

Now Malakal is populated mainly by soldiers, with large houses and NGO offices requisitioned for the war effort. Most civilians have fled. More than six months after the government regained control of the town, over 17,000 people still live in the grotesquely swollen UN base a 10 minute drive from the main urban area, coping as best they can with their temporary shelters, the lack of hygiene, and the reality of their newly reduced circumstances.

Some of the displaced cautiously make their way into town during the day, to sell goods in the market, or check on what is left of their houses. Most believe it is still too dangerous to leave the camp.

Those now living in muddy squalor in the UN base are, like the population of Upper Nile state itself, mainly Nuer, Dinka and Shilluk. Their interactions inside and outside the UN base mirror the shifting dynamics of politics in the state.

In the years before independence, there was considerable frustration in the Shilluk kingdom, which borders the White Nile around Malakal. Many complained that their land had been stolen by the Dinka, with the support of the ‘Dinka-dominated’ SPLA. Several Shilluk self-defence groups sprang up.

Tensions increased during the 2010 elections. South Sudan’s major opposition leader, Lam Akol, is a Shilluk, and received considerable support from his home region, increasing the perception within the SPLM/A that the area and its people represented trouble. Shilluk politicians within the SPLM, including Pa’gan Amum, then the Secretary General of the party, lost popularity at home because of their apparent inability to help ‘their’ people in a time of need.

Armed resistance grew. In March 2011, in the run-up to independence, a Shilluk militia leader, Johnson Olony, attacked Malakal town. He eventually joined the South Sudan Democratic Movemement/Army (SSDM/A), a loose coalition of rebel groups backed by Khartoum, and became its leader after the death of George Athor. However, in June 2013, Olony accepted a presidential amnesty, reportedly after receiving an ultimatum from the Shilluk king.

Six months later, South Sudan slid into civil war. As thousands of SPLA soldiers (predominantly Nuer) defected to him, Riek Machar could have been forgiven for hoping for significant reinforcements from among the Shilluk. They, too, had many grievances with President Salva Kiir’s government. If sizable Shilluk forces, perhaps led by Olony, had turned on the government, Machar’s chances of hanging on to Malakal, and over-running the Paloich oilfields to the north, would have increased considerably. This did not happen.

Shilluk chiefs, elders and others told me that things could have been very different if Machar’s forces had stopped their bloody march at Malakal in the early days of the war. Instead, the rebels attacked several Shilluk villages, on both banks of the White Nile.

“We were surprised when the Nuer came and killed our people,” says Jok Wanh Adiang, a sub-chief in the small town of Wau Shilluk, a 20 minute boat raid north of Malakal, which is now home to thousands of Shilluk displaced. “It’s very bad.” The chief of Wau Shilluk, Obieny Jako Adhok, says that “when the Nuer came, we thought it was to fight Dinka. But when they arrived, they came and killed Shilluk and looted property. So that’s why the Shilluk didn’t join the rebels.”

Instead, Olony’s forces played a major role in the government campaigns to regain control of Malakal. At the otherwise muted Independence Day celebrations in July, Olony, a giant man, received warm cheers. He told the crowds that he had a “doctorate in fighting”, both a boast about his military prowess, and a rebuke to the academically-qualified Shilluk politicians who have not protected and developed the area.

According to the chiefs, Olony is actively recruiting Shilluk into his forces. The men are given ‘the price of soap’, small incentives, rather than a salary. They are seen not as a component of the SPLA, but as a ‘Shilluk self-defence force’, the chiefs say. As elsewhere in South Sudan, the creation of ethnic militias, while an understandable counter-insurgency strategy, is deeply damaging to the cohesion of the nation.

The politicians in Juba and Addis Ababa usually say that ethnicity is not a driving factor in the conflict. Although this may have been true at the very outset, a succession of atrocities targeting one ethnic group or another, in Juba, Bentiu, Bor, Malakal and elsewhere, make it harder and harder to deny that ethnicity is at least part of the equation. And very often, lower-ranking officials, civilians and traditional authorities identify ethnic animosity or community self-preservation as the key motivation for the fighting.

Some of those tensions are felt inside the UN base. Nuer camp dwellers in general are too scared to go into town, which is controlled by the SPLA and Olony’s forces. They also know they are mistrusted by the other displaced people: “because I am from Nassir, they think I am with the rebels”, says one. In February, several people were killed as fighting outside the camp brought skirmishes within. Since then, the divisions have largely been kept under control. The end of the rainy season is likely to bring more conflict in Upper Nile state, and may raise the temperature within the camp too.

The fighting has also strengthened the desire of many Shilluk to call for greater autonomy, a wish that, ironically, is also the ideology of the federal system demanded by Riek Machar. Sitting on a plastic chair outside a makeshift shelter in the UN camp, a social worker and respected elder, Stanislas Obul, tells the story of the Hyena, the Leopard, the Lion and the Snake, who end up killing each other. “These are the animals that cannot live together”, he says, before referring explicitly to the Nuer and the Dinka.

Obul, like the chiefs in Wau Shilluk, and others in Upper Nile state, argues for greater independence for the Shilluk and by extension everyone else in South Sudan – a larger terrain in which the dangerous animals will not have to mingle. This may not happen – and it may not be desirable, given the danger of creating ‘tribal islands’ which would dilute any sense of a strong national identity. But certainties in South Sudan are being swept away by the day.

James Copnall is a journalist and author of “˜A Poisonous Thorn in Our Hearts: Sudan and South Sudan’s Bitter and Incomplete Divorce’. He is editor of ‘Making Sense of the Sudans’.