When history repeats itself for a third time, it is beyond tragedy. Since its independence fifty-one years ago, Sudan has suffered two civil wars between North and South, each of them as bloody as–and much longer than–today’s crisis in the western region of Darfur. Quietly, Sudanese military planners are preparing for a third round of that war. Just two weeks before violent clashes erupted in the Southern city of Malakal at the end of November, Salva Kiir, the president of Southern Sudan–who is also first vice president in Sudan’s Government of National Unity–issued a stark warning: “The war will return to the South if peace is not achieved in Darfur, and that is really our fear.” He repeated the warnings in a speech January 9, the second anniversary of the agreement that brought peace to Southern Sudan. Kiir’s alarm is good reason to intensify international efforts over Darfur–but he is also putting us on notice to pay attention to a looming nationwide crisis.

There’s no doubt that President Omar al-Bashir and his cabal of security chiefs bear the major responsibility for bringing Sudan to its current state of despair. Certainly urgent action is needed to stop the killing in Darfur, which first aroused the conscience of the Western world in 2003, spurring a well-organized mass movement and student campaign to “save” the region. The impulse among Western activists and policymakers to entertain regime change, and to pressure and punish those whose misdeeds have inflicted so much death and destruction, is understandable. But punitive and interventionist measures carry a high risk of sparking intensified conflict or bringing about government collapse–either of which would have calamitous humanitarian consequences. American leadership to avert such disasters is needed now.

While the crisis in Darfur has captured the attention of Western activists, that conflict developed partly because of the incomplete resolution of the North-South war. And both conflicts arose from the same general phenomenon: regional discontent with exploitation, of both people and resources, by the central government in Khartoum. The Darfur crisis can neither be understood nor resolved apart from the more deep-rooted North-South confrontation.

When Sudan won its independence in 1956, a rebellion was already under way in the South. Southern Sudanese, black and overwhelmingly non-Muslim, feared that national independence simply meant a replacement of British imperial rule by Northern Sudanese Arab colonialism. Their fears were well founded, as Southerners suffered discrimination and abuse from Northern governments seeking to create a Muslim and Arabized country. This war lasted seventeen years, until a peace accord was signed in 1972. A decade’s interlude of peace followed, but the political travails that marked those years–including half a dozen attempted military coups–cemented Sudan’s reputation as Africa’s most dysfunctional country.

A second war broke out in 1983. The Sudan People’s Liberation Army (SPLA), headed by John Garang, fought four successive governments in Khartoum until, with major effort from Kenya, the United States and Europe, a Comprehensive Peace Agreement was signed in January 2005. Commonly known as the Naivasha Agreement, after the Kenyan resort where negotiations were conducted, the CPA promised the democratization of Sudan and an equitable distribution of oil revenues between North and South. Its greatest weakness is that despite the word “comprehensive,” the accord didn’t deal with the war in Darfur. That conflict had erupted just as the North-South war was finally coming close to settlement.

The Darfur rebellion arose out of a sorry history of misgovernment and the region’s unfortunate location next door to Chad’s civil war, which has alternately smoldered and blazed since the 1960s. Twenty years ago Khartoum turned a blind eye to Libya’s use of Darfur as a rear base to attack Chad, and the depredations of the Chadian Arab militia it had armed–the original Janjaweed. As law and order collapsed and Darfurian tribesmen acquired weapons to defend their farms and herds, Khartoum failed to act as an honest broker in the numerous local conflicts. On the contrary, it policed Darfur by promoting loyal chiefs and arming their militias. Most of these loyalists were Arabs who fueled Arab supremacist ideology and underwrote an escalating land grab. By 2003 a coalition of village self-defense groups trying to hold on to their land and educated Darfurians incensed at the region’s marginalization in national politics came together as the Sudan Liberation Army and mounted a guerrilla war. Garang encouraged the SLA, hoping that a new insurgency in the west would press Khartoum to make bigger concessions on his agenda of a radical “New Sudan.”

Garang miscalculated: As the rebellion in Darfur surged–and especially when dissident Islamists set up a second Darfurian rebel front, the Justice and Equality Movement–Bashir unleashed a savage counterinsurgency that killed tens of thousands of civilians, caused many more to die of hunger and disease and displaced more than 2 million. This was more than disastrous coincidence: It highlighted the main flaw in the Naivasha process, which is that in setting up a new government of national unity, it privileged Khartoum’s ruling National Congress Party (NCP) and the South’s SPLA while leaving out Sudan’s other political players–most critically, those from the Darfur region.

When Garang signed the CPA with Vice President Ali Osman Taha in January 2005, he had remedied many of the defects in the 1972 agreement. The South was to have its own government, development budget and law (Islamic law still holds sway in the North). A government of national unity was created, giving the NCP the presidency and 52 percent of seats in the National Assembly and Cabinet, with Garang’s party taking the vice presidency and 28 percent. The remaining seats are divided among numerous other parties–a share most of them consider unfairly small. But the CPA promises free nationwide elections in 2009. It also gives Southerners the chance to vote on unity or an independent Southern Sudan in 2011 and–an essential guarantee–it allows the SPLA to remain as the Southern army during this interim period.

Why did Khartoum and its undefeated army accept these huge concessions? The key was Vice President Taha, who sold the peace accord to his skeptical colleagues in government as the country’s last chance for unity and as the path to ending Sudan’s international isolation–especially the lifting of sanctions imposed by the United States dating back to Bashir’s 1989 coup and Khartoum’s hosting of Osama bin Laden from 1990 to 1996. For its part, the US State Department backed Taha as the best chance for a peaceful end to the war and as an ally in the “war on terror.” Garang’s Southern critics were doubtful, but in the end they rallied behind the peace deal. “He has one vote,” says one pro-independence Southern politician, “among 7 million.” Southerners had learned patience, and when the date for the referendum on self-determination came six years on, they would vote with their hearts–for independence.

Just a few months after the CPA was signed, Garang’s helicopter crashed into a mountain on the Uganda-Sudan border, in July 2005. Southern Sudanese rioted, and Northern liberals who had long cherished the dream that Garang could bring a modern democracy to their country quietly mourned. Garang’s successor as first vice president in the Government of National Unity, Salva Kiir, has made reconciliation among Southern factions his priority; only in recent weeks has the SPLA begun to build a national political party to contest elections.

Taha had gambled that peace would create a new politics in Sudan. But when Garang’s body was laid to rest, Taha’s star dimmed sharply. As Khartoum’s party operators and security chiefs realigned themselves amid the flux of intra-elite intrigue, it became clear that few in the Cabinet believed in the spirit of the CPA. Without strong leadership to rein it in, the security cabal reverted to its vicious games, fomenting discord among the Southern tribes and going slow on giving the South its half share of the oil revenues.

To salvage his strategy of unity through democracy–and to save his own political skin–Taha now needed the United States to deliver on its promise of improving relations between Washington and Khartoum. But the United States would not move on this until there was a deal on Darfur. Having initially seen the Darfur conflict as little more than an irritating sideshow to the North-South war, the Administration was pressed by an unprecedented mobilization of college students and community groups, who branded Darfur “the first genocide of the twenty-first century” and insisted that the United States had a responsibility to stop it. This mass movement scored some impressive victories: Colin Powell labeled the Darfur killings “genocide” in September 2004, the case was referred to the International Criminal Court by the UN Security Council in March 2005 and the White House handed down an instruction that there should be a peace deal and that the small African Union peacekeeping contingent should be upgraded to a sizable UN force.

Taha’s hope was that an accord with the largest of the Darfur rebel groups–the SLA, headed by Abdul Wahid al-Nur–would translate into an electoral pact that would allow the NCP to emerge from the 2009 elections as head of a ruling coalition. This was a tricky piece of political engineering to pull off–not only did Taha have to convince the rebels; he needed to get his own government behind the plan. Indifferent to whatever moral condemnation was heaped upon them, Khartoum’s security chiefs were intent on a new military offensive, confident that by fomenting insurrection in Chad they would cut off the rebels’ rear base and force them to submit.

After months of painfully slow negotiations, last May a combination of African leaders, US Deputy Secretary of State Robert Zoellick and a host of other international diplomats managed to obtain the signatures of Khartoum and Minni Minawi (chief rival to Abdul Wahid in the SLA) on the Darfur Peace Agreement. But against the wishes of most of his delegation, Abdul Wahid refused to sign. A little more flexibility by the African Union and the United States might just have pulled off a deal, but Abdul Wahid was also banking on outside military intervention that would drive the Sudanese army from Darfur. He was ill advised–he should have known that neither the United States nor the Europeans were ready to commit to fighting Khartoum’s army on his behalf.

The Justice and Equality Movement also refused to sign. They and other holdout factions began a military offensive last summer. The Sudanese army has tried to enlist the Minawi faction as its shock troops, but without much success. More ominous for Khartoum, many among Darfur’s Arab tribes–most of which have until now remained neutral in the conflict–are shifting toward the rebels. (The depiction of the Darfur war as “Arabs” versus “Africans,” always simplistic, is becoming more and more of a misrepresentation as the conflict drags on.) But although they are winning the battles, the holdout rebels are politically fragmented and have no plan for what to do with their military momentum. Most of them want to go back to the negotiating table, but they won’t do so unless they get the chance to revise the text of the Darfur Peace Agreement.

Khartoum hasn’t stuck by its commitments under the agreement. There has been no effort to disarm the Janjaweed militia, and the one rebel signatory, Minawi, has been given no real power. The relative lull in fighting of 2005 has been replaced by escalation in many areas. Although the level of atrocities is still far below what happened when the government-Janjaweed counteroffensives rampaged through North and West Darfur three years ago, lawlessness is now at such a level that humanitarian operations are more restricted than at any time since those dark days. Should relief access deteriorate still further, the health and lives of millions will be threatened.

The African Union peacekeepers–a mere 7,000 troops to cover a territory as large as France–cannot stop the violence. Taha had signaled that Khartoum would agree to a handover from the AU to an enlarged UN force, but when the UN Security Council passed Resolution 1706 last August 31, authorizing 20,000 blue helmets–and implying that it might impose them without Khartoum’s consent–President Bashir overruled his more accommodating colleagues and army generals and drew a red line. He categorically rejected UN troops in Darfur, thereby cementing Taha’s marginalization, and ominously declared that the Sudanese army would bring peace to Darfur.

Bashir fears that UN troops would have an open-ended mandate to arrest anyone indicted by the International Criminal Court and that authorizing international troops to use force on his territory would be a Trojan horse for a takeover à la the US invasion of Iraq. In naming the first two war crimes suspects on February 27, the ICC was carefully respectful of Sudan’s sovereignty, giving Bashir the opportunity to cooperate in handing over the two men. But he is unlikely to take this way out–as long as he believes the Western agenda is one of regime change, no pressure in the world will be sufficient for him to yield. What he has reluctantly conceded is a limited role of UN support to the existing African Union force. Recent diplomatic arguments have been over the makeup of such a force, but there’s no strategic plan for how to achieve stability in Darfur. Security cannot be imposed with 20,000 troops, or even 100,000 troops, in the absence of a peace agreement. An effective peacekeeping operation will be nine parts community liaison and political intelligence to one part force. This requires a long-term vision of how peacekeepers will work with tribal chiefs and the men who run village self-defense groups to bring security, peace and reconciliation to the region. But what’s needed first is a political deal.

In January UN special envoy Jan Eliasson promised to reconvene talks with the rebels. The plan as it stands today sounds suspiciously like the failed formula from last May: a deadline to sign on to a document the rebels don’t want to accept. Bitter and fragmented but militarily confident, the rebels are no easier to negotiate with than Khartoum’s wily leaders. For anything to work, the steps must be taken in the right order: cessation of hostilities, a rebel conference to choose new representatives, proper monitoring of a cease-fire and confidence-building steps, and then negotiations–with a credible mediator and sufficient time to hammer out the issues. Shortcuts will just bring more failure.

As Darfur’s travails continue, Sudanese confidence in the North-South democratization process promised in Naivasha is ebbing. The spirit of peace and democracy that infused the accord is gone, and there’s no strategic plan for how to revive it–or cope with its absence. The signs of possible collapse are worrying. At the end of November, a disagreement over who should take a senior army post in the Southern town of Malakal led to a fierce battle between the SPLA and a militia group that had been backed by Khartoum during the war and still retains its links with military intelligence. Peace was restored by the prompt action of both commands and the intervention of UN peacekeepers, but not before more than 300 people, many of them civilians, had been killed. The clash wasn’t planned, but it showed the vulnerability of Southern Sudan to irruptions of violence.

Disputes over security arrangements are the most likely flash point, but there are others. The commission for demarcating the North-South boundary has not begun its work. The most contentious area is Abyei–an enclave of ethnic Southerners historically administered as part of the Northern region of Kordofan–where an independent commission has produced a border ruling that Khartoum categorically rejects. Lucrative oil concessions lie precisely in this disputed area. In addition, the key condition for a free and fair election, a credible national census, has yet to begin. Under these conditions, elections might themselves be the focus of violent conflict, and Khartoum’s lawyers may dream up any number of reasons for rejecting the results of a referendum on self-determination that doesn’t go their way.

Resolution of Sudan’s crises must be guided by two realities. The first is that a popular vote for separation of the South is far more likely than a vote for unity. Most Southern Sudanese say they are waiting patiently for the 2011 referendum. If that vote is free and fair, most will vote for independence. The wishes of the Southern electorate must be respected and the outcome implemented smoothly and peacefully. But planning for the transition should begin now. The best option is to explore the possibilities for mutually advantageous coexistence by future new states of Southern and Northern Sudan. This requires a pre-referendum pact insuring Khartoum’s legitimate economic and security interests in the South, along with the South’s interests in the North. If this or something similar isn’t done, the prospects for massive bloodshed and humanitarian crisis are dark.

The second reality is that Khartoum’s security cabal and NCP operators are sufficiently powerful that they can thwart any plan if their core interests are not taken into account. The choice will be between a soft landing for Bashir and a new conflict that puts at risk the peace of Naivasha and deepens the crisis in Darfur. Opinion polling is not advanced in Sudan, but internal surveys by Northern political parties indicate that a coalition government will be needed. It would be reasonable to begin working on a pre-election pact insuring that the NCP will remain a part of any such coalition, and that there is consensus on the key policy questions facing the new government. If there’s an agreed end-state that guarantees a role for Bashir, it will be possible to exert pressure on him to play by the rules. But no amount of sanctions and threats will push him down a road he believes will lead to his demise.

Bashir and his cabal have been pushed to the wall by economic and political sanctions before, and survived. They can do so again–their funds, now considerably swollen by increased oil revenues, are hidden away in Saudi and Swiss bank accounts. A no-fly zone in Darfur is a more realistic option. In the security arrangements chapter of last May’s Darfur Peace Agreement, Khartoum already committed itself to ending hostile military flights and allowing intrusive monitoring of its air bases–provisions that add up to a no-fly zone and that could be implemented more simply than overflights by NATO fighters. On the other hand, last October’s proposal by former Clinton Administration officials Anthony Lake and Susan Rice for a Kosovo-style bombing campaign would in reality be a declaration of war on Sudan, with incalculable consequences. It is much better to focus our energies on reconvening talks on Darfur, alongside new attention to salvaging the Naivasha Agreement. The core principles of power-sharing, democratization and self-determination for the South should be inviolable, but the means for realizing these goals must be re-examined.

After the ravages of Sudan’s first civil war, it should have been unthinkable for Northern and Southern leaders to contemplate resolving their differences through force of arms. But war creates war. The military mentality had become so embedded among Sudan’s politicians that fighting was not only thinkable, it was the default option. Today, despite the palpable disasters brought by a history of unremitting violence, there are still men ready to fight, or to order others to fight. Leaders on both sides know that a new war would be a catastrophe for all. It would begin with violence in the cities and lead to the disputed secession of the South. The certainty of such disaster has not prevented warmakers in the past and will not do so again. What can prevent it is a coordinated strategy for a stable, managed transition to democracy. That, we do not have.