One thing is clear about the new war in the Nuba Mountains region of South Kordofan, the first war of the shrunken Republic of Sudan presided over by President Omar al-Bashir: No one outside Sudan knows how to address it. Most wish it would simply go away – that those pesky Nuba would put down their arms in the interest of the “larger peace” between the two Sudans and make the best of living in a separate, northern state that Bashir has said will have no room for cultural and ethnic diversity.

That is not going to happen. The determination of the Nuba to fight against underdevelopment, inequality and marginalization – including by arms if necessary – has been strengthened both by the strong showing of the Nuba fighters of the Sudan People’s Liberation Movement/Army (SPLM/A) North in the first two months of the war, and by the promise of wider military alliances with others opposed to Khartoum.

Ever since the Khartoum government and the SPLA signed a peace agreement in 2005, ending two decades of civil war, South Kordofan’s neighbor, Blue Nile, has been the most peaceful of the areas monitored by United Nations peacekeepers. Although twinned with South Kordofan in a special protocol in the agreement, and having many ethnic and political similarities with it, the SPLA in Blue Nile has so far left the Nuba to fight alone. That may be about to change. In the last month, Malik Agar, an SPLA veteran who is now governor of Blue Nile, has said repeatedly that he cannot sit on his hands for much longer. He has warned that the Nuba war will spread, igniting a front that will extend from Darfur to the Ethiopian border, unless agreements signed with South Kordofan and Blue Nile are honored.

Agar was the key figure in negotiations between the Khartoum government and SPLM North that produced a new framework agreement for South Kordofan and Blue Nile just 23 days into the South Kordofan fighting, raising hopes of a negotiated settlement. Bashir reportedly sees him as a man with whom he can do business.

If Blue Nile explodes – whether because Khartoum attempts to disarm the SPLA by force, as it did in South Kordofan, or because Agar decides to support the Nuba – the SPLM North will be banned in Sudan and all chance of negotiation will be lost for the foreseeable future. Blue Nile is of enormous strategic and economic importance: Three-quarters of all Nile waters enter Sudan through it, and Sudan’s biggest irrigation schemes depend on the Blue Nile dam at Roseires. Widened violence could draw in regional actors including South Sudan and Ethiopia, Blue Nile’s eastern neighbor and early SPLA ally.

Alarm bells should be pealing. They do not appear to be. Instead Khartoum’s generals believe they can win a showdown in Blue Nile and have convinced some of their interlocutors that this is indeed the case. Anyone tending to this belief should revisit Agar’s record on the battlefield, notably his defense of Kurmuk in May 2001. Outmanned and outgunned, he ordered a tactical retreat before circling behind the government forces and attacking them from the rear, destroying them.

The Sudanese armed forces made a similar miscalculation in South Kordofan two months ago, and were both surprised and humiliated at their string of losses to the Nuba SPLA.

Fighting had no sooner erupted in South Kordofan on June 5 than commentators were pinning labels on it: “ethnic cleansing,” “extermination,” “genocide.” According to this version of history-in-the-making, the baddies with pale skins are doing what they do best – killing Sudanese with black skins – and will only realize the game is up when white-skinned saviors ride in with bigger guns.

Without question, Bashir’s regime has a proven record of waging brutal wars against civilians in the name of Islamism and Arabism. But this is no straightforward repeat of the Nuba jihad of the 1990s or the Darfur war of the last decade. Politics in post-secession northern Sudan is driven by a new dynamic, one largely invisible to outsiders who shun Khartoum’s powerbrokers, because their lawyers prohibit them from meeting with individuals named by the International Criminal Court. A new configuration is propelling the new fighting – hinted at by the SPLM North in a statement in which it cited “the domination … of the military junta” over the leadership of Bashir’s National Congress Party (NCP).

The SPLM did not elaborate. But a well-informed source close to the NCP reports that Sudan’s two most powerful generals went to Bashir on May 5, five days after 11 soldiers were killed in an SPLA ambush in Abyei, on South Kordofan’s southwestern border, and demanded powers to act as they sought fit, without reference to the political leadership.

“They got it,” the source says. “It is the hour of the soldiers – a vengeful, bitter attitude of defending one’s interests no matter what; a punitive and emotional approach that goes beyond calculation of self-interest. The army was the first to accept that Sudan would be partitioned. But they also felt it as a humiliation, primarily because they were withdrawing from territory in which they had not been defeated. They were ready to go along with the politicians as long as the politicians were delivering – but they had come to the conclusion they weren’t. Ambushes in Abyei … interminable talks in Doha keeping Darfur as an open wound … Lack of agreement on oil revenues …”

“It has gone beyond politics,” says one of Bashir’s closest aides. “It is about dignity.”

This will not be an interpretation of the current conflict accepted by those who see a genocidal arc stretching from Darfur to South Kordofan. But it is perhaps something the international community could reflect upon as it debates how to get negotiations back on track – even if only in the interest of the “larger peace.”

Julie Flint writes frequently on Sudan for THE DAILY STAR.