Last week, the low intensity conflict between the new state of South Sudan and the Republic of Sudan escalated into a near full-scale war. On Monday April 10, the Sudanese Peoples’ Liberation Army (SPLA) took control of the strategic town of Heglig from troops loyal to Khartoum. That same day, Khartoum launched a series of air rides, bombing the towns of Jonglei and Heglig. In the ensuing fight, SPLA shot down two of Khartoum’s MIG 29 jets.

(Read: Khartoum promises to wage war over Heglig)

On Wednesday April 11, the United Nations Secretary-General, Ban Ki Moon, called the President of South Sudan, Salva Kiir Mayardit, saying “I am ordering you to pull your troops out of Heglig.” On Thursday morning, Kiir addressed parliament in Juba where he told a cheering crowd that he had told Mr Ban on the phone, “I am not under your command.” The United States ambassador to the United Nations, Susan Rice, called on both parties to cease hostilities. As the week ended, South Sudan was in full military mobilisation.

The war between North and South Sudan is swiftly becoming a complex international issue; Khartoum accuses the SPLA of launching aggression on its territory and supporting rebels in Blue Nile and South Kordofan; that is why it has retaliated by bombing South Sudan’s positions. Technically, Khartoum is right, for the troops fighting it are SPLA soldiers — to be precise, soldiers of the SPLA North, which fought alongside the Southern army between 1983 and 2005. But Juba denies involvement in the war in North Sudan, as the SPLA North soldiers are actually not from South Sudan. It is this part of the jigsaw puzzle that has to be understood if international efforts to end the conflict are to bear fruit.

Khartoum has a reputation for exclusion, marginalisation and oppression of many communities in its territory. The civil war in Sudan that led to the signing of the Comprehensive Peace Agreement in 2005 pitted many of these marginalised communities against Khartoum. Given its oppressive ways, one could even say that most of Sudan has been marginalised by the Khartoum regime. However, the more distinctly marginalised groups included people in the territory currently known as South Sudan, South Kordofan (where most of the intense fighting has been taking place) and eastern Sudan, especially the areas around the Red Sea Mountains. This region is occupied by different communities close to the Ethiopians and Eritreans. In fact, eastern Sudan is the poorest and most marginalised region of the Republic of Sudan. And finally, there is Darfur, the best known conflict in Sudan.

The territory currently known as the Republic of South Sudan was a separate entity from the rest of modern day Sudan until 1947, when the British colonial government integrated it into Sudan. Although this is the region where the SPLA was born, it was not the only region with grievances against Khartoum. Thus, when SPLA was formed, communities from South Kordofan, Nuba [Southern Kordofan is in the same Nuba mountains] and the Blue Nile region that had grievances against Khartoum joined the SPLA. Even marginalised groups from Darfur who did not form part of the SPLA received inspiration and training from it. Therefore, by the time the CPA was signed in 2005, communities from these regions other than Darfur formed two divisions of the SPLA.

These divisions of the SPLA remained inside North Sudan. When Khartoum failed to meet their demands, they launched a war of liberation too. Khartoum has used this to claim that it is under attack from South Sudan and has won sufficient international support with this claim. Secondly, it has also used it as an excuse to attack South Sudan, now an independent state, thereby triggering off an international war.

Knowledgeable sources say that many of these communities felt betrayed by the SPLA when it signed the CPA, which paved way for the Independence of the South from the rest of Sudan. They had fought alongside the SPLA for more than two decades and felt that the Independence of South Sudan would leave them in a relatively weaker position. However, sources say, the main faction of the SPLA that formed the new South Sudan promised to pressure Khartoum to reach an agreement with its former allies in these marginalised regions. It also promised them support if Khartoum failed to accommodate their concerns. But Khartoum seems to have had little interest in addressing the grievances of these communities. The question is why?

Contrary to what people think, Khartoum had a strong interest in the secession of South Sudan. This seems contradictory because most states prefer to hold onto territory even at extremely high cost. This is especially so for Khartoum because most of the oil (80 per cent) is in South Sudan; so one would expect it to fight tooth and nail to keep the South. Yet there were many more complex factors that seem to have driven the National Congress Party of Omar Al Bashir, the current President of the Republic of Sudan, to want to shed South Sudan. The reality for him was either to lose power altogether or lose the South.

However, this interest was not one way. There were people in the SPLA from South Sudan who wanted to leave the union. But the SPLA was never united on this issue and in a series of internal debates, the movement accepted a compromise that created an opportunity for unity and if that did not work, to go for Independence. Therefore, there was a convergence of different but compatible interests between Khartoum and the South Sudan faction of the SPLA/M for separation.

By the time the CPA was signed, the only marginalised part of the wider Sudan that had developed both the military and political capacity to effectively challenge Khartoum was South Sudan. To put it the other way, the most militarily and politically strong faction of the SPLA/M was the one largely drawn from the South. Khartoum seems to have calculated that if it got rid of South Sudan, it would effectively break the SPLA/M down the middle, separating the strong part from the weaker one.

In Khartoum’s calculus, this would mean that the most effective fighting machine of the SPLA would have little interest in helping the other marginalised regions to fight the NCP regime. The remaining rump of the SPLA/M inside the older Sudan would now be weak and easy to crush. It is this calculation that drove Bashir to sign the CPA, seeing it as an opportunity to rid himself of a major threat, weaken internal resistance and open the way for him to subdue what remained of that resistance.

Meanwhile, within South Sudan, there were differences too on how to deal with their allies from the other regions of Sudan. Some people in the SPLA/M felt that they should not abandon them. But doing this would undermine progress towards Independence and perhaps drag the war on for many more decades. In fact, sources say, former SPLA leader John Garang wanted to keep a unified Sudan. He only signed the CPA, which recommended Independence for the South, because it had a clause clearly stating that both the North and the South should work for unity.

Admirers and enemies in the South and North say Garang was ambitious and wanted to be president of a bigger entity than a small “fiefdom” called South Sudan. However, there were other voices led by Kiir, Garang’s deputy and current president of South Sudan. These felt that unity was an unrealistic ideal and separation a more realistic objective. The clause that both sides should work for unity and separate if that ideal failed to work was the key compromise between the Garang and the Kiir camps of the SPLA/M that made the CPA possible.

Although the NCP under Bashir wanted separation, many people in Khartoum did not support this objective. While the regime extremists wanted a forcibly united country, the common people wanted separation to end the war. Thus, many political forces opposed to Bashir saw in Garang a patriot willing to keep the country united. They wanted an inclusive democratic government, which they hoped Garang would provide as he forged alliances with the West and the East. These opposition forces now became internal surrogates of Garang in Khartoum. Thus when he went to the capital to be sworn in as vice president under the CPA in May 2005, Garang was welcomed as a hero by both the “African” and “Arab” elite and rank and file. One million people turned up in Khartoum to give him a heroes’ welcome, a factor that was not missed by the Bashir regime and some forces inside the SPLA/M who preferred secession.

When Garang died two months later, it was the final nail in the coffin of a united Sudan under Khartoum. The new SPLA/M leader, Salva Kiir, was deeply committed to separation. In an ironic twist, Kiir’s greatest ally was Bashir and his apparatchiks inside the NCP. Kiir wanted secession not only because he did not think unity was a viable option but also because he did not want the South to share its oil wealth with people who had suppressed them for years. Bashir wanted secession because it would help him get rid of his strongest enemy from the union.

But this path did not resolve the problem of the other marginalised groups that formed a weak but significant portion of the SPLA. Southern Kordofan is populated by Nubians, whose freedom fighters are led by Abdel Aziz Al-Hilu. In Blue Nile, the fighters are largely from the Funj tribe, and are led by the former governor of the state, Malik Agar. How were those SPLA divisions drawn from South Kordofan, Nuba and Blue Nile going to be handled? Would it be up to South Sudan to disarm them? Would they become an independent entity with whom Khartoum could negotiate? But before all these issues could be digested, there was an issue to deal with first.

In 2011, there was a general election in the whole of Sudan. SPLA had promised to contest the elections and actually fielded a candidate, but an unknown entity called Yassir Arman. Salva Kiir himself kept out of the election in order, many observers now say, to ensure that Bashir won — because he wanted a separate South and going for the seat in Khartoum would be too risky, given the likelihood that the election would be rigged. Second, even if he won, he was only be in the seat for about seven months. Then he would have to go home to his village after secession since there would be a different president in the South. Many people say that if Garang were still alive he would have contested the election. If he did, it was very likely that he would have won as he would have attracted the votes of all the marginalised communities and the votes of many Khartoum Arabs who preferred a united Sudan.

Indeed, this was evident in the fact that the SPLA candidate Arman turned out to be a strong contender in the election for president. Realising that he was likely to win, the SPLA pulled him out of the race three weeks to the election. Yet in spite of this, Arman got 21 per cent of the vote. One can only speculate how much Garang would have got had he been alive and decided to run in that election.

This also means that had Kiir run, he would most likely have beaten Bashir hands down. However, critics of Kiir say he lacked the high ambition and self-confidence to aspire to rule the whole of Sudan. They accuse him of securing a deal with Bashir that allowed both of them to capture their own fiefdoms.

However, supporters of Kiir say he was much more foresighted and realistic than Garang. They argue that sections of the North that hated Bashir wanted to keep the South not because they love unity but because of its oil. They had been unable to unseat Bashir and saw in Garang an instrument they could use to get rid of their rival. According to this view, the army, police and all security agencies of the old Sudan are controlled by the Northern “Arabs” as are the bureaucracy, judiciary, diplomatic service, education, and healthcare. Had a Southerner been elected president, he would have been unable to change the entire system overnight. So he would become a hostage of these deeply entrenched interests, who would be strong enough to sabotage his plans or even kill him.

Kiir’s supporters further argue that in his big vision of a united Sudan and his ambition to lead it, Garang was blind to this fundamental reality that would have made him an ineffective president unable to serve the interests of the South. The best way to serve the people of the South was Independence, as this would give them an independent nation with oil revenues to sort out many of the issues dear to their people. It is this argument that tilted the dice in favour of Kiir and his supporters. But how would the South handle those in its ranks who came from the other marginalised regions? SPLA promised to urge Khartoum to negotiate with them.

Although South Sudan has asked Khartoum to find accommodation with these SPLA fighters, Khartoum has consistently dodged the issue. Thus, when these rumps of the SPLA decided to renew the civil war against the regime in Khartoum, the reason why Bashir was dodging negotiations with them became apparent. Rather than accept responsibility for the war or see it as an internal rebellion against the policies of his government, he accused Juba of launching an aggressive war against his government — a perfect excuse.

The situation in Sudan is exactly like the one that Uganda faced in October 1990 when remnants of the Ugandan army crossed the border and attacked Rwanda. Then, former Rwandan president Juvenal Habyarimana argued that the Ugandan army had invaded his country. Technically he was right. But in fact, the soldiers were Rwandan refugees who had been living in Uganda and had joined the Uganda army. They had decamped from it without permission to launch their own war against his regime. But Habyarimana was able to use this “evidence” to convince the world that his country was under attack from Ugandan troops.

Using highly skilful media propaganda, Khartoum has been able to effectively convince the international community that it is South Sudan that has invaded Northern Sudan. It is in this context that Mr Ban called President Kiir to demand that South Sudan troops withdraw from Northern territory. This is the more intriguing given that up till now, Khartoum has resisted all attempts to clearly demarcate the border between the two countries, making it difficult to establish whether the positions that the SPLA troops under the command of Juba have entered are in the North’s territory or not.

But most critically, Khartoum has been able to hide the fact that it is not South Sudan but its own people who have taken up arms against it. But how will pressure on South Sudan by the international community solve the internal problem of the demands by groups in South Kordofan, Blue Nile and Nuba regions for equitable treatment and inclusion? Thus, as things stand, the conflict between Juba and Khartoum is only a sideshow, a smoke screen to hide the more fundamental issue of the demands of other marginalised regions inside the old Sudan.