As southern Sudanese celebrate their self-determination referendum, spare a thought for those they leave behind – all those in northern Sudan for whom the birth of an independent state in the south of the country will be the death of a dream: the democratic, decentralized “New Sudan,” united and free of racial, ethnic or religious prejudice, which was the stated aim of the Sudan People’s Liberation Movement/Army (S.P.L.M./A.) under the leadership of John Garang.

Conventional wisdom has tended to be that the National Congress Party (N.C.P.) of President Omar al-Bashir would fight tooth and nail to prevent the South seceding. Prominent commentators, especially in the United States, have warned that another “genocide” was on the cards. One went as far as to say the violence was likely to resemble “what happens in a stockyard.” Instead, Bashir recently traveled to the southern capital, Juba, on the eve of the vote and promised “to respect the choice of the citizens of the South.”

The North-South understanding is of course fragile. There are many flashpoints, many spoilers, and many people in Khartoum who think Bashir has given away too much (a third of the country, three-quarters of national oil production, and much rich grazing land that is of critical importance to northern pastoralists). Generally, however, the approach of the president’s N.C.P. seems to be that the S.P.L.M. has set secession as its objective, and the N.C.P. will accept it, but also make the price very high.

Part of the price is that the S.P.L.M. will not be permitted to continue as a political party in the North. The S.P.L.A., the armed wing of the S.P.L.M., will be permitted no presence – except for a minority that could be integrated into the Sudan Armed Forces (at the discretion of the N.C.P., and on its terms). The S.P.L.M. and its international backers must accept that they will have no role or access across the new border after partition.

Already there are signs that the N.C.P. is closing down in terms of tolerating dissent in the North – military offensives in Darfur, arrests of journalists and activists in Khartoum, inflammatory statements from the very top of the N.C.P., especially regarding the future of southerners in the North. Notice to quit has been served on the United Nations peacekeeping force, or U.N.M.I.S.

There is special concern among the Nuba people of Southern Kordofan state, “African” tribes at the southern limit of the Arabized North, many of whom fought alongside the southern S.P.L.A. for 15 years, at the cost of tens of thousands of lives. A special protocol in the 2005 Comprehensive Peace Agreement (C.P.A.) that ended the civil war failed to satisfy the aspirations of S.P.L.M. supporters in the Nuba region and the second “protocol state,” Blue Nile – most importantly, their demand for self-determination.

The Nuba war was a civil war in its own right, an indigenously mobilized rebellion with strong local roots. With international attention focused on the conflict in southern Sudan, Khartoum sealed the region off from 1991 until 1995. At its height, the war was not only a war to defeat the rebels; it was a program of forced relocations designed to empty the mountains and resettle the Nuba in camps where their Nuba identity would be erased. Humanitarian access was denied. Educated people and intellectuals were detained and killed, according to a security officer who later fled the region, traumatized by what he himself had overseen. The aim, as he recalled, was “to ensure that the Nuba were so primitive that they couldn’t speak for themselves.”

After 1991, cut off even from the S.P.L.A. in southern Sudan, the Nuba fought alone, without resupply from the South. In the middle of a three-year famine, they established a civilian administration and judicial system, organized a religious tolerance conference, and took a popular vote on whether to fight on or surrender.

The unique nature of the rebellion was one of the reasons why the Nuba became something of a cause célèbre for a few years, once the atrocities of the government’s war in the mountains were exposed. Then came the C.P.A., and the war in Darfur. The Nuba fell off the agenda and implementation of the provisions relevant to them in the C.P.A. was neglected – jobs, development, and, critically, the formation of a new national army incorporating S.P.L.A. units.

On July 9, the C.P.A. will end – and with it the agreements that determine the fate of the Nuba people. A leaked N.C.P. document has identified them as “new southerners,” who must be “weakened … controlled [and] pulled out at the roots.” Secessionists, in other words. Rightly or wrongly, many Nuba fear the worst, beginning now.

The promised “popular consultations” for the two protocol states to review C.P.A. implementation remains a weak and ill-defined mechanism that can be drawn out indefinitely by disagreement with the center – even if the concept survives a North-South split. Southern Kordofan needs more than a popular consultation. It needs an internationally mandated mechanism to oversee implementation of unfulfilled C.P.A. commitments beyond the end of the C.P.A. It needs agreement on a new international presence, with examination of non-U.N. options in case Khartoum remains opposed to U.N. troops. It needs security mechanisms acceptable to and involving S.P.L.A. units. Northern Sudan as a whole needs the democratization the C.P.A. promised to deliver, but didn’t.

Southerners may feel they have won their battle. Northerners have not.

Julie Flint, co-author, with Alex de Waal, of “Darfur: A New History of a Long War,” has written extensively on Sudan for THE DAILY STAR.