On July 9, 2011, tens of thousands of South Sudanese gathered in the capital city of Juba at the mausoleum of rebel leader John Garang to celebrate the creation of their new state. Six months earlier, these jubilant crowds had voted in a referendum for independence from northern Sudan; more than 98 percent cast their ballots in favor of secession.
On the intensely hot and sunny day, men in suits and military uniforms and women in dresses stood in the stands, mopping their brows, listening to speeches by South Sudan’s new president, Salva Kiir, and other heads of state. Those who did not faint in the heat observed a myriad of military processions and marching bands and watched as Sudan’s flag was lowered and that of South Sudan was raised. Boisterous cheers erupted as the new flag reached the top of the pole, women ululating with gusto.
Among the speakers that day was Susan Rice, US Permanent Representative to the United Nations and a long-time advocate of the rights of the southern Sudanese. “Our support for the cause of peace for the Sudanese people has long been bipartisan and deep,” she said, “and it will continue to be. We helped broker the Comprehensive Peace Agreement that led us here today, and we will continue to watch over it — and the future to come.”
Indeed, the US played a significant role in brokering the Comprehensive Peace Agreement (CPA) that formally ended two decades of civil war between the Sudanese government and the southern Sudan People’s Liberation Movement/Army (SPLM/A). US diplomacy revived the multilateral negotiations hosted by Norway, Great Britain, Italy and the Intergovernmental Authority on Development (IGAD), and US negotiators took the lead in shaping much of the agreement’s terms.
Concern about Sudan had been growing in the US since the late 1990s, with various groups — from humanitarian activists to the oil lobby to the Christian right — voicing their desire for increased American involvement in the conflict. By early 2001, the influential think tank the Center for Strategic and International Studies (CSIS), through a “Task Force on US-Sudan Policy” that included academics, government officials and other think tank leaders, had produced a report recommending engagement with Sudan in order to rejuvenate the peace process. Newly elected President George W. Bush took up the Sudan cause in large part due to outspoken evangelical leaders who continually highlighted a vision of the conflict in which a Muslim north oppressed a Christian south. This view of Sudan as a “clash of civilizations” helped solidify a narrative that made secession the more likely — though not necessary — outcome of the CPA.
The CPA Falls Short
The CPA was an eleventh-hour effort to find a lasting solution to the two-decade civil war between the northern elite-dominated central government and the poor regions in the south. Various government programs since the late 1950s had attempted to Arabize and Islamize the country through the education system and the imposition of Islamic law, though nearly 30 percent of the population — largely those living in the south — are non-Muslim, including a small percentage of Christians. The first armed conflict between southern rebels and the northern army ended with the Addis Ababa Agreement of 1972, but a second civil war began in 1985. The northern government organized and armed militias to suppress rebellion in the south, destroying villages and abducting women and children and forcing them into slavery in the north. Conflicts between rival factions and splinter groups of the SPLM/A also killed thousands. Approximately 2 million people died and 4 million were displaced during the war — most of them from the southern and central parts of the country.
The CPA greatly reduced attacks against civilians in the south, but the agreement also included provisions for oil revenue sharing, disarmament and democratic elections that were never realized. National elections were delayed until 2010, but were plagued with irregularities. Six major opposition parties boycotted the elections and the SPLM only participated in parliamentary and local races in the Blue Nile and South Kordofan provinces. President Omar al-Bashir and the National Congress Party continued to rule with a corrupt and authoritarian fist. The CPA, however, included the “escape clause” of the referendum, which gave the southern Sudanese the right to vote for secession six years after the signing of the agreement.
While the CPA would ideally have set up a democratic system throughout the whole of Sudan, the slow implementation and numerous violations of the agreement ensured that the six-year interim was more like a waiting period than a time of transformation. Both northern and southern Sudan, of course, played significant roles in this missed opportunity. According to Alan Goulty, former British Special Representative for Sudan, the two sides simply could not cooperate: “They continued to treat each other as antagonists.”  The CPA dictated that the country’s oil income was to be split evenly, but the south accused Khartoum of not living up to its end of the bargain, keeping hundreds of millions of dollars in profits for itself. The two sides also could not agree on the demarcation of the north-south boundary—a point of contention still in play today in the border area of Abyei. During this period, the SPLM, which had always dominated southern politics, became even more entrenched as the sole political partner of the central government.
Many point to the death of John Garang in a helicopter crash six months after the signing of the CPA as another principal reason for the political shift toward secession. Garang led the SPLM/A with a vision for a united Sudan, one “of full equality, without discrimination on the grounds of race, ethnicity, religion, culture or gender.”  Salva Kiir, the SPLM vice president who succeeded Garang in the unity government, was a vocal advocate for southern independence.
Tango with Bashir
Back at the independence ceremony on July 9, Omar al-Bashir was in attendance; many in the crowd reacted to his arrival with boos and surprised murmurs. The American delegation at the ceremony was also displeased with al-Bashir’s presence, and the late Rep. Donald Payne, a Democrat from New Jersey, told the Washington Times beforehand that if the delegation made plans to meet with the Sudanese president, “I will not attend.” Though no meeting occurred, anxiety about the seating arrangement abounded. South Sudanese officials choreographed the event such that African delegations that had been sympathetic to al-Bashir sat on his side of the dais, while Western and non-African delegations sat next to Salva Kiir.
Such American queasiness about al-Bashir, who was charged by the International Criminal Court in 2009 with war crimes and crimes against humanity in Darfur and in 2010 with three counts of genocide, is not a new phenomenon. The US relationship with Sudan goes back to its independence from Britain in 1956, but no American administration — even when Cold War obsessions meant the US either cozied up to or rejected Sudan, depending on how its government was leaning — has seen the country as vital to its interests. While Chevron discovered oil in southern Sudan in the late 1970s, the relatively small reserves never made access to Sudanese oil a “front-burner issue” for the US.  Containing radical Islamist groups in Sudan, however, became a priority of the Clinton administration. In the 1990s, following al-Bashir’s 1989 coup, Sudan was known as a safe haven for terrorists, including Osama bin Laden, who built up al-Qaeda in Khartoum from 1991 to 1996. In the late 1990s, in succession, the US imposed economic sanctions on Sudan, al-Qaeda attacked US embassies in Kenya and Tanzania, and the US bombed a Khartoum pharmaceutical plant. From 1998 to 2000, little contact between the two countries occurred; President Bill Clinton aimed to isolate Sudan, meeting with rebel groups but failing to form a multilateral coalition that would help the US pressure the regime.
In 2000, Clinton’s special envoy to Sudan, former Florida congressman Harry Johnston, as well as a US Counter Terrorism Dialogue Team that traveled to Khartoum, brought back news that al-Bashir and his government were ready to renounce support for terrorist groups and work with the US on counter-terrorism initiatives.
At first, it looked like George W. Bush would not bother much with this opportunity. While campaigning for the presidency that same year, he made it clear that he would not focus on Africa if elected. “While Africa may be important,” he said, “it doesn’t fit into the national strategic interests.”  In the first two months of his presidency, however, Bush publicly referred to Sudan three times — not in terms of terrorism, but in regard to the country’s lack of religious freedom, human rights violations and humanitarian crisis. Even more surprisingly, in late January 2001, only weeks after assuming the presidency, Bush began a review of US Sudan policy.
The Weekly Phone Call
Many interpreted these events as being directly related to Bush’s status as a born-again Christian and his closeness to evangelicals, particularly Rev. Franklin Graham — the son of Billy Graham and a vituperative critic of the Sudanese government. Both Grahams had been known to call Islam “evil and wicked,” and Franklin, who ran a Christian hospital in Blue Nile, had announced that Sudan’s northern government was “genocidal.” 
Melani McAlister has pointed out that as the Cold War ended, evangelicals concerned about the persecution of Christians shifted their focus from the threat of Marxism — “the twentieth century’s scourge on religion,” according to one conservative leader — to another menace, Islam.
Particularly after the fall of the Berlin Wall, evangelical leaders began to concentrate their missionary work on new regions, especially the “10/40 window,” the area between 10 degrees and 40 degrees north of the equator — which includes the Middle East and most of Asia. They turned to the secular language of human rights to further their cause, dramatically highlighting cases in which Christians in countries such as Sudan, Iran, Ethiopia and Egypt had been killed, maimed, abducted or simply taunted by Muslims for their faith. More moderate and liberal evangelicals, as well as Catholics, began to get on board.
In 1996, Nina Shea, a Catholic who was then director of the Puebla Program at Freedom House, penned one of the burgeoning movement’s “manifestos,” In the Lion’s Den: Persecuted Christians and What the Western Church Can Do About It, in which she stressed that Islam and the surviving Communist world were the two main global concerns for Christians. In 1997, Shea and other adherents were fighting for US legislation that would focus on stopping the persecution of people for their faith by requiring immediate action against any nation found in violation.
The more rigorous bill did not survive opposition from big business interests, liberals who warily viewed it as concerned only with Christians, and President Clinton, who wanted to be able to avoid tough action when it suited him. The less stringent International Religious Freedom Act (IRFA), however, passed in 1998 and required annual lists of “countries of concern.” Interested parties could closely follow the actions of the government in regard to those countries.
After IRFA’s enactment, a frenzy of books, magazines and other publications circulated that depicted Christian suffering at the hands of Muslims, with Sudan at the forefront of offenders. In 2001, the new US Commission on International Religious Freedom — set in place by IRFA and on which Shea has served continuously — declared Sudan “the world’s most violent abuser of the right to freedom of religion and belief.”  Ten years later, Shea, now a senior fellow at the conservative Hudson Institute, continues to emphasize the religious elements of Sudan’s north-south conflict. “It’s really quite startling,” she said. “The north used every method it could to kill people in the south, and it converted those it enslaved to Islam…. It’s really a religious and ethnic fault line running through Sudan.” 
The ascension of George W. Bush to the presidency occurred during the period just after IRFA passed, and Bush’s religious leanings and friendship with Franklin Graham ensured that he became personally involved. According to a US government official, Bush and Graham spoke weekly about “what to do with Sudan.” “Bush actually cared about the place,” the official said. “You could never fault the guy for not caring.” Bush and Graham’s weekly chats were indicative of the larger phenomenon of a strong evangelical lobby that connected with a number of religiously inclined members of Congress, notably Republican Sens. John Danforth of Missouri and Sam Brownback of Kansas. The official also noted that the SPLM/A understood the potential of a rallying cry in the name of religion. “The SPLM effectively used Christianity and the bad Muslim/good Christian narrative to generate support for their cause in the US,” he said. 
The evangelical lobby and the senators who championed its cause, as well as Bush’s personal investment in Sudan, therefore shaped US policy by framing the civil war as a “clash of civilizations” between Islam and Christianity. While Bush ended up split in his loyalties between his evangelical constituency and furthering the war on terror, the idea of the Muslim north persecuting the Christian south was never questioned. As such, the popularized framing of the conflict between northern and southern Sudan as one between bad Muslims and good Christians stayed firmly in place and led to policies based on simplistic notions about the Sudanese.
A Sudan Divided
The roots of this conceptual split lay in Sudan’s colonial history. In 1899, Britain and Egypt established a condominium — a jointly governed territory — in what is present-day Sudan. Though the condominium arrangement stipulated that Britain and Egypt were to govern as partners, from the beginning Britain effectively ruled Sudan as its own colony. The British administered the colony in two parts: northern and southern, with the goal of modernizing the north and simply bringing the south under its control. During the first 25 years of rule, a group of British military officers nicknamed the “Bog Barons” ran the south as district officials. The Barons reportedly “went native,” living for many years in the same district and identifying with the people they ruled. The central government in Khartoum left the Barons alone, with the result that “few attempts [were made] at modernization [in the south].”  In contrast, the British opened schools and expanded railways, telegraph services and steamer lines in the north.
In the late 1920s, the central government took more of an interest in the south, and aimed to set up a system of indirect rule there in which southern “racial and tribal units” would administer areas based on “indigenous customs, traditional usage and beliefs.”  The British believed Muslims and Arabs would erode these indigenous customs if southerners regularly mixed with them, so they “sealed off” the south from the north, repatriating northern merchants and military officers. The colonizers also believed this strategy would safeguard against the spread of Islam southward along the Nile. Christian missionaries had been proselytizing in the area for years with the intent of converting those with animist belief systems.
These colonial policies drew upon categories of racial and religious identity that were already in place within the Western-drawn boundaries of Sudan, but they oversimplified a complex situation and reinforced the dichotomy that pits “northern Muslim/Arab” against “southern Christian/African.” Recent pre-secession statistics help clarify the more complex nature of Sudan’s population. Only 5 percent of Sudanese citizens are Christian, according to the CIA World Factbook, and these are found “mostly in [the] south and Khartoum.” Seventy percent of the population is Muslim (found in the north), and 25 percent hold indigenous beliefs. Francis Deng, a prominent Sudanese academic and politician, has consistently argued against the ideas of “racial, cultural and religious homogeneity that oversimplify and falsify a dynamic picture of pluralism.” 
Sudan’s British colonial history thus set the scene for a Western preoccupation with a divided Sudan. But the evangelical Christian movement that focused its efforts in the country in the late twentieth century helped solidify the mythology of Muslim north versus Christian south.
Seeing an opportunity in Bush’s election, evangelical and other, more secular, interest groups stepped up their criticism of Sudan, encouraging Bush to increase pressure on the government. A number of these groups, including the Enough Project, an initiative to prevent genocide through the Center for American Progress, supported regime change. Some evangelicals urged Bush to “arm the Christian rebels” and support their “fight for separation” from the Muslim north. But Bush, taking the advice of his special envoy to Sudan, John Danforth, decided that engagement with al-Bashir and his regime was the best option. Indeed, Sudan, acting on its word from the previous year, was quick to condemn the September 11, 2001 attacks and subsequently apprehended suspected terrorists.
Though Bush kept Sudan on the state sponsors of terrorism list and continued implementing US sanctions, some evangelicals were not mollified. They retaliated with a letter signed by more than 100 religious and civil rights leaders pressing Bush to be more severe with Sudan and to endorse the Sudan Peace Act sponsored (in an unusual partnership) by Republican Christian members of Congress and the Democratic Congressional Black Caucus. Bush tried to block the act, which aimed not only to badger al-Bashir’s government with sanctions but to provide monetary support to the rebels, but it passed in 2002 and put enough pressure on the regime that it likely helped ensure al-Bashir’s unenthusiastic cooperation with the CPA.
Other Sudan observers in the US, including CSIS, shaped US policy toward a peace agreement that included a mechanism for the south to secede. In early 2001, CSIS produced a report on US Sudan policy that recommended engagement with Sudan, as well as an “interagency task force to advance analysis and planning of a self-governing south and marginalized northern groups.”  Though other regional struggles against the central government received mention, CSIS argued that ending the civil war was a prerequisite to addressing these other conflicts. (The importance of securing an agreement before the north had the opportunity to fully develop the oil industry was also stressed.) The report came out of a task force funded by the US Institute of Peace that was co-chaired by Stephen Morrison of CSIS and Francis Deng. Morrison, who had been with the Clinton administration for seven years, said, “It had become apparent that the Clinton era policy of isolation/marginalization and hope of regime change had failed.”  Others who agreed and successfully took the agenda to the Bush administration included Republican Rep. Frank Wolf of Virginia and Walter Kansteiner, who was made assistant secretary of state for African affairs in June of that year.
The US then took the lead role in negotiations, working with but also eclipsing the long-time principal actors. US officials made sure that the referendum was part of the Machakos Agreement of 2002 — the agreement that helped pave the way for the CPA. In initial meetings that year, Kenyan IGAD mediator Gen. Lazaro Sumbeiywo and his colleagues drafted a text that did not include the right of self-determination for the south. “Not only was the SPLM furious, the US envoy walked out of the talks,” writes John Young, who evaluated the peace process for IGAD in 2007.  Ultimately, the agreement included the referendum vote after a waiting period — similar to the course laid out in the CSIS report and to what the CPA would dictate three years later.
Bush increasingly had to manage the desires of his important conservative Christian constituency and his own desire to extract cooperation from Sudan in the war on terror. He and his administration eventually won over a good number of evangelical groups by avidly listening to (if not always acting upon) their concerns. Over time, many came to accept engagement, and other, more secular advocacy groups’ calls for no-fly zones and regime change became more muted. Though the agreement that emerged from these competing demands continued engagement with al-Bashir, it also provided the opportunity for the “Christian separation” that evangelical leaders had called for — and thus a kind of compromise was reached.
This idea of “Christian separation” was evident in the US policy community’s habit of treating the conflicts in Sudan in a piecemeal fashion, rather than as variations on a common theme, namely, “the violent hoarding of wealth and power at the center of the country at the expense of the periphery,” in the words of one US official.  As a result, the US did not address the north-south conflict as related to numerous other rebellions against Khartoum, such as those in Darfur and eastern Sudan, as well as in the border areas of the Blue Nile state and South Kordofan, but instead as a clash between Islam and Christianity.
Realizing the Referendum
Ambivalence about engaging al-Bashir continued into President Barack Obama’s administration. Though Obama talked tough about Sudan during his presidential campaign, advocating a NATO-enforced no-fly zone in Darfur and chiding Bush for negotiating with Khartoum, he continued working with al-Bashir’s regime on anti-terrorism initiatives as president. By the time Obama took office in 2009, it was apparent that the CPA’s mandate for democratic elections and other cooperative provisions were not coming to pass. “It was abundantly clear for several years that the south Sudanese were going to vote for secession,” notes Jonathan Temin, director of the US Institute of Peace’s Sudan program. As such, maintaining a relationship with al-Bashir was necessary to ensure that the agreement’s “escape clause” could be carried out. Adds former special envoy to Sudan Andrew Natsios, “Without al-Bashir, there wouldn’t have been a referendum. He’s more of a realist than others in [his party].” 
Of course, not everyone in Obama’s administration felt as charitably toward al-Bashir. In 2009 then-Special Envoy to Sudan Scott Gration riled Sudan activists — particularly those concerned about the situation in Darfur — when he declared, “There is no evidence in our intelligence community that supports [Sudan] being on the state sponsors of terrorism [list].” Sam Brownback spoke up on the Senate floor not long after Gration’s announcement: “What happens next time an individual is involved in a genocide? Do we say: If you start behaving a little less worse on your genocide, we will start to give you some carrots?… I say no. I say we cannot do this.” And David Sullivan, research director at the Enough Project, said that the appointment of Gration brought about a “worrisome situation” in which Gration and other members of Obama’s administration, notably Susan Rice, clashed on Sudan policy — issuing diverging statements on whether what was occurring in Darfur was a genocide. Rice called the genocide “ongoing,” while Gration averred it was in “remnants.” 
Yet these disagreements revolved around the issue of whether to use carrots (the Gration camp) or sticks (the Rice camp) with al-Bashir and thus demonstrated that all were in support of seeing the referendum through. Even John Prendergast of the Enough Project — the organization that had previously been more of an advocate for regime change — was firmly in the Rice camp, writing in a New York Times op-ed in 2010 with author Dave Eggers that more sanctions and other pressures should be applied to al-Bashir’s government to force cooperation vis-à-vis the referendum.
It must be said that without the implementation of the CPA and its referendum, the situation in Sudan would likely have remained status quo ante. At least, many say, the south now has a chance. But the focus on separation rather than democratic reform has set both states down an uncertain road. In 2010, Kiir won 93 percent of the vote in an election characterized by voter intimidation and harassment of rival political parties. Since independence, several journalists have been arrested for criticizing Kiir and the government. Limited and uneven development in the south has also underscored communal violence in the eastern state of Jonglei that has killed several hundred and displaced thousands since August 2011. The south’s exit from Sudan has left other turbulent areas under the thumb of a nervous al-Bashir afraid of losing more of the country. The results, pre- and particularly post-secession, have been bloody, with the Sudanese government occupying the contested border area of Abyei and waging war in Blue Nile and South Kordofan — and accusing the SPLA of arming the rebels there.
In early November 2011, South Sudan, supported by UN officials, accused the north of bombing South Sudan proper — hitting a camp near the border that housed more than 20,000 displaced persons. Al-Bashir has denied all charges, and expressed his government’s willingness to go to war to stop the SPLA from arming rebels. In Darfur, sporadic fighting continues between rebels and government-armed militias and among rebels themselves. Such conflicts continue, despite Khartoum and Juba signing a non-aggression pact in Addis Ababa in early February 2012. On November 1, Obama renewed US sanctions against Sudan, though Sudanese leaders — and some US observers — had counted on them being lifted as a reward for allowing secession. (While the sanctions on southern oil, which is brought to market through the north, were lifted on December 8, the south began shutting down its oil fields in January 2012 after accusing the north of stealing hundreds of millions of dollars of its oil. Al-Bashir and Kiir have both suggested that armed conflict will arise unless a deal can be reached.)
The US response to these new developments has been to point out belatedly that the conflicts in (northern) Sudan must all be dealt with as part of the same problem—of Khartoum oppressing its periphery. While policymakers certainly understood this issue long before now, it is intriguing to note that the notion is being bandied about publicly only post-secession, rather than ten years ago when it might have changed the course of US policy in Sudan and the creation of the CPA and its “escape clause” for the south. “It’s awfully easy to criticize in hindsight,” said Temin. “For instance, if we had tried to wedge Darfur into the CPA, it might not have happened at all.”
Post-secession, it appears that US policy toward Sudan is beginning to change in a fundamental way. In October 2011, Princeton Lyman, the current special envoy to Sudan, made remarks to the House of Representatives Subcommittee on Africa, Global Health and Human Rights in which he called attention to the fighting in South Kordofan and Blue Nile. “These two states are still in Sudan, not South Sudan,” he said, “but the political issues underlying the conflict there have the same roots as the civil war that ended with the CPA, and which should have been resolved in that context but were not.” And Prendergast, in a return to championing democratic change in the north, also pointed to this issue in a paper released in early August 2011. “US efforts to promote peace in Sudan have been undermined by a fatally flawed premise: that separate peace deals could be secured for each of Sudan’s multiple conflicts without finally dealing with the divisive, autocratic regime in Khartoum,” he said.  Temin co-wrote a report in June 2011 asserting a similar point of view.
Perhaps now that the war has (formally) ended, the perceived Muslim/Christian divide has been realized and evangelical groups have been appeased, it has become politically possible to approach Sudan’s conflicts as a whole rather than in fragments. But, whether positive democratic change can come about in northern Sudan while al-Bashir and his party retain their stranglehold on power is, according to Temin, “the million-dollar question.”
 Alan Goulty, “The New Sudan: Challenges and Opportunities,” Carnegie Endowment for International Peace, February 9, 2010.
 Francis Deng, Sudan at the Brink (New York: Fordham University Press and the Institute for International Humanitarian Affairs, 2010), p. 7.
 Telephone interview with Jonathan Temin, October 2011.
 Raymond L. Brown, “American Foreign Policy Toward the Sudan: From Isolation to Engagement,” unpublished Ph.D. dissertation, National Defense University, 2003, p. 3.
 Ibid., p. 24.
 Quoted in Melani McAlister, “The Politics of Persecution,” Middle East Report 249 (Winter 2008).
 Interview with Nina Shea, Washington, DC, May 2011.
 Interview with anonymous US government official, Washington, DC, May 2011.
 Robert Collins and Francis Deng, The British in the Sudan, 1898-1956: The Sweetness and the Sorrow (Stanford, CA: Hoover Institution Press, 1984), pp. 11-13, 15.
 Sir Harold MacMichael, “Memorandum on Southern Policy, January 25, 1930,” quoted in Collins and Deng, pp. 23, 27.
 Francis Deng, “War of Visions for the Nation,” in John Voll, ed., Sudan: State and Society in Crisis (Bloomington, IN: Indiana University Press, 1991), p. 26.
 J. Stephen Morrison and Francis Deng, “US Policy to End Sudan’s War: Report of the CSIS Task Force on US-Sudan Policy,” Center for Strategic and International Studies, February 2001.
 E-mail correspondence with J. Stephen Morrison, February 1, 2012.
 John Young, “Sudan IGAD Peace Process: An Evaluation,” May 30, 2007.
 E-mail correspondence with US government official, November 10, 2011.
 Interview with Andrew Natsios, Washington, DC, May 2011.
 Interview with David Sullivan, Washington, DC, May 2011.
 John Prendergast, “New US Policy Needed for Sudan, South Sudan,” Enough Project, August 4, 2011.