The Bentiu massacre in mid April, in which hundreds of people died, has become one of the defining images of the new civil war in South Sudan. TV pictures of bodies lining the streets of the town, and piled up in a bulldozer to be taken for burial, went around the world. The United Nations says that, among other atrocities, at least 200 people were killed and 400 wounded at the Kali-Ballee mosque. There are differing accusations about who was responsible, but there is no dispute that many Sudanese were among the dead. Nearly three years after Africa’s biggest country split in two, the destinies of the two Sudans – and their peoples – continue to be tightly linked.

The UN has pinned the blame for the massacre on the South Sudanese rebels, more formally known as SPLA/M in Opposition, under the overall command of the former Vice President, Riek Machar. They are accused of killing those believed to support President Salva Kiir, including Nuer (despite most of the rebels themselves being Nuer), non-Nuer, and foreigners: Sudanese.

The rebels have rejected the accusations. Yet even the official rebel statement of denial accepted that Sudanese had been killed. In this account, the Sudanese were soldiers from a Darfuri rebel group fighting for Kiir. The statement claimed ‘members of Sudanese rebels of the Justice and Equality Movement (JEM) fighting for Salva Kiir’s government wore civilian clothes during the two-day clashes in and around Bentiu. The bodies of their dead colleagues, almost all men, were also collected and piled up during the night for the purpose of claiming them to be foreign civilians rounded up and executed in such places by our gallant forces.’

Sudanese human rights groups have rejected this, saying the dead were civilians, for the most part traders, who had sought refuge in the mosque (and Bentiu’s hospital, where others were killed). A large crowd of Sudanese, particularly Darfuri traders, protested in the South Sudanese city of Wau after the news of the massacre emerged. They too said that those who had been killed in Bentiu and the neighbouring town of Rubkona were unarmed civilians.

Whether the South Sudanese rebels killed JEM fighters in civilian clothes, or massacred civilians on the basis of their nationality, and supposed ethnic or regional connections to JEM, one of the principle motivations was JEM’s military role in South Sudan. JEM, and other Sudanese rebel groups, most notably SPLM-North, have received backing from Juba. The SPLM-North is fighting the government in South Kordofan and Blue Nile. It would find it extremely difficult to survive without its supply line over the border into South Sudan. The Darfuri rebels, JEM, established a base in Unity state in the new country. From here, JEM has been able to strike north into Sudan, and in particular into the Kordofan region, as its sphere of operations shifted away from Darfur.

In the post-separation period, Sudan also backed South Sudanese rebels, including Bapiny Monytuil, James Gai Yoach, George Athor and others who spent most of their time in Khartoum. Monytuil’s house was in Kalakla Wihda, in the south of the Sudanese capital, for example, before he eventually accepted an amnesty agreement and returned to Juba. South Sudanese living in Khartoum were press-ganged into these militias, leaving thousands too scared to go the building sites and universities their friends had been snatched from. David Yau Yau twice rebelled against the South Sudanese government in Jonglei state, rallying hundreds of Murle to his side. He was supported by Khartoum too. Both countries used rebels to fight a low level proxy war, undermining the old enemy on the other side of the new border.

Since civil war broke out in South Sudan in December last year, there have been many accounts of JEM fighting alongside SPLA troops loyal to Salva Kiir. An International Crisis Group report states that ‘JEM fought Riek Machar’s forces twice in Pariang (an important trade hub for them), supporting the government’s efforts to retake Bentiu, Unity state. It is also alleged to have helped recapture the Unity oil fields, which JEM leaders deny. JEM was also involved in the SPLA’s campaign to re-take areas in southern Unity state, including Machar’s home area.’ Parts or all of this account have been variously confirmed to me by UN, security and religious sources in Unity state. JEM is repaying its debt to Juba, and must also hope to gain weapons and supplies in combat and in return for its efforts.

The great irony in all this is that the man JEM has sworn to overthrow, Sudan’s President Omar al Bashir, has publicly supported his South Sudanese counterpart Kiir, placing JEM and Bashir as uneasy neighbours on Kiir’s side of the table.

In the immediate post-separation period, the relationship between Juba and Khartoum was extremely bad. Bitter negotiations over oil, the disputed border, the region of Abyei, citizenship and security issues made little or no progress in Addis Ababa. Both Sudans attempted to destabilise the other, not just by supporting rebel groups, but also economically. Sudan shut the border, cutting off trade with the new state. South Sudan shut down its oil industry after Sudan started grabbing oil in lieu of payment for the use of pipelines, refineries and an export terminal with which South Sudan got its oil to market. The economies of both countries staggered, but did not totally collapse.

The effect on the peoples of the two Sudans was dramatic: poverty rates increased; development projects were put on hold. The millions of people in the Tamazuj or ‘intermingling’ area either side of the new border suffered particularly, but sometimes were able to maintain much healthier ties than those between the political elites. Far from the capitals, the border dwellers complained about the high prices which resulted from Juba and Khartoum’s decisions, visited relatives and fought enemies across the international frontier, and negotiated safe seasonal passage into South Sudan for the Misseriya and Rizeigat and their cows.

In April 2012, SPLA and SAF, each backed up by the other’s rebels, fought on the disputed border, most notably at Heglig. In hindsight, this was the lowest moment of the post-separation relationship. The threat of UN sanctions contributed to the Sudans signing nine Cooperation Agreements in September 2012, including on oil, trade, citizenship and the creation of a demilitarised buffer zone on the border. Eventually the oil started to flow again. There was a further blip after the Sudan Revolutionary Front attack on Abu Kershola in April 2013, because Khartoum blamed the rebel alliance’s success on South Sudanese support; but Bashir eventually withdrew his threat to close the oil pipelines again. Kiir’s visit to Khartoum, in August 2013, confirmed the new, wary friendship, based on an understanding that both political elites would benefit if the oil kept flowing, and the border hostility was kept to a minimum.

When the civil war broke out in South Sudan, Khartoum had a decision to make. Sudanese diplomatic sources claim Machar offered a share in oil profits in return for military help. Instead Bashir visited Juba to announce his backing for the elected President. Some in the South Sudanese government are worried that Khartoum could shift its stance, particularly if the military balance alters. The Sudanese were certainly unhappy about the Ugandan troops – and JEM – fighting against Machar’s rebels so close to their border. Nevertheless, Khartoum is unlikely to switch sides while the oilfields remain out of Machar’s complete control.

Khartoum’s choices will have a great impact on the course of the South Sudanese civil war, and Juba’s position on South Kordofan, Blue Nile and Darfur is vital too. Beyond elite politics, the border peoples will continue to depend on each other. They, and everyone else in the Sudans, know that the economies of the two countries are intertwined. Separation was not a clean rupture, but a messy divorce.

James Copnall is a journalist and author of “˜A Poisonous Thorn in Our Hearts: Sudan and South Sudan’s Bitter and Incomplete Divorce’.