A boy wears a T-shirt with the face of U.S. President Barack Obama in Koch, southern Sudan on Nov. 13, 2010. Credit: Roberto Schmidt/AFP/Getty Images







JUBA, South Sudan — A vicious bloodletting was already underway by the time President Salva Kiir appeared on television dressed in military fatigues. It was the afternoon of December 16, 2013, and the South Sudanese capital had been a war zone for more than 12 hours. Kiir wore an officer’s patrol cap instead of his trademark black Stetson — a gift from John Kerry to replace the one George W. Bush had given him in 2006 — and trudged through his remarks with terse diction. If there had been any hope that he could halt his country from sliding into all-out civil war, the embattled president quashed it with a single rhetorical flourish: After implying that his former vice president, Riek Machar, had attempted a coup, Kiir declared ominously that he would “not allow the incidents of 1991 to repeat themselves again.” To the outside world, the reference might have seemed cryptic. But in South Sudan, the message was crystal clear: 1991 was the year Machar broke away from the main southern guerilla movement, the Sudan People’s Liberation Army (SPLA), that was fighting against the Sudanese government in Khartoum. The move nearly brought about the SPLA’s demise. Now, Machar was again estranged from the flock and about to mount a new rebellion from the bush. By linking the two events, Kiir was invoking an old and powerful grudge. “It was not in the spirit of reconciliation,” Lam Akol, who led the breakaway SPLA faction with Machar in 1991 and later served as Sudan’s foreign minister, told me. “It was a declaration of war.” "It was not in the spirit of reconciliation. It was a declaration of war." During and after Kiir’s press conference, forces loyal to the president rounded up and executed hundreds of male Nuers, the ethnic group to which Machar belongs. The soldiers reportedly identified the men by asking their names in Dinka, the language of Kiir’s ethnic group; inability to answer could be a death sentence. In one neighborhood, according to Human Rights Watch, between 200 and 300 men were detained in a building used by police and then murdered by gunmen, alleged to be members of the South Sudanese armed forces, who fired on the prisoners through windows. Machar denied the coup allegation, but as Juba descended deeper into violence, he quickly took up arms against the government. Soon, blood was flowing across the northeastern portion of the country: in Bor, the capital of restive Jonglei state, and then in Bentiu and Malakal, two major cities in the heart of South Sudan’s oil country. Reports of war crimes committed by both sides followed. Over the next year, somewhere between 10,000 and 50,000 people would be killed and another 2 million forced to flee their homes. Farmers missed their planting season, and aid agencies warned of an impending famine. According to the United Nations, the humanitarian crisis created by South Sudan’s civil war is now on par with those in Syria, Iraq, and the Central African Republic. “I never thought I’d see the day when people would be fleeing to Darfur,” Toby Lanzer, the top U.N. aid official in South Sudan, told me in August. “But that’s the situation we’re in.” A few days after my meeting with Lanzer, I boarded a U.N. plane in Juba packed with peacekeepers and other humanitarians and flew several hundred miles north over swampland and jungle to Malakal, roughly tracing the path of the violence that had exploded across the country. Control of the city had changed hands between the government and Machar’s rebels six times in nine months, and some of the worst atrocities of the civil war had been committed there. The last time rebels overran the city, they burned so much of it that satellite imagery revealed charcoal smudges where whole neighborhoods once stood. Now, the government was back in charge, and it was flooding troops and equipment in ahead of the dry season, when fighting in South Sudan has historically taken place. Rumors abounded of an impending rebel attack. After a brief stop at the U.N. base near Malakal, where roughly 20,000 civilians were waiting out the violence in overcrowded displacement camps, I caught a ride with UNICEF employees down the rutted dirt track to what used to be South Sudan’s second-largest city. The closer we got, the fewer civilians there were. In the center of town, where abandoned market stalls sat bleakly on patches of scorched earth, the only humans in evidence were government soldiers, most of them carrying AK-47s. When we passed the sagging bungalow that used to serve as UNICEF’s living quarters, half a dozen armed men grinned out at us. Like most structures that hadn’t been destroyed, the building was occupied by the South Sudanese army. March 2014: Rebels and defected SPLA soldiers loyal to former vice president Riek Machar, in a controlled territory of Malakal city. People help an elderly woman evacuate from her hut in Malakal. Credit: Mohammed Elshamy/Anadolu Agency/Getty Images We drove past looted warehouses, shelled government buildings, and rows of thatched huts that had been put to the torch. Not far from the obliterated central market, the ruins of a teaching hospital spilled out into the street: smashed vials, soiled bandages, and now-useless medical equipment. In February 2014, at least 14 people were murdered there when rebels swept into Malakal. The day before our arrival, I was told, staff members discovered a body rotting on the roof of one of the hospital’s annex buildings. While we toured a gutted pediatric complex across the street, I nearly stepped on a skull that was hidden in the grass. Slogging through what was left of Malakal, it was difficult to imagine that South Sudan was once considered a major U.S. foreign-policy success. Over a span of nearly two decades, three different U.S. administrations worked to bring the new nation into being. Bill Clinton was the first to signal support for the southern separatists battling Khartoum in the Second Sudanese Civil War, which lasted more than 20 years and left an estimated 2 million people dead; his administration unlocked military support for neighboring countries that was then funneled covertly across borders. George W. Bush later made Southern Sudan a centerpiece of his foreign policy, helping broker a landmark north-south peace deal in 2005 that ended the civil war and paved the way for southern independence. The Obama administration carried the ball across the goal line, ensuring that an independence referendum went ahead as planned in early 2011 and pouring hundreds of millions of dollars in development aid into the new country. When South Sudan finally hoisted its own flag in Juba on July 9, 2011, someone waved a sign that read, “Thank You George Bush.” When South Sudan finally hoisted its own flag in Juba on July 9, 2011, a delegation of Bush and Obama administration officials was in attendance. In the crowd, the New York Times reported, someone waved a sign that read, “Thank You George Bush.” Now that South Sudan has imploded in spectacular fashion, however, it offers a case study in the limits of American power: Not only have its tremendous state-building efforts failed to bear fruit, but the U.S. government now finds itself with virtually no ability to shape events on the ground. “We’re at an all-time low in terms of influence,” said Cameron Hudson, who worked on South Sudan policy in both the Bush and Obama administrations. To be sure, the new nation faced long odds. At independence, it had virtually no civil institutions, about 120 doctors for a population of roughly 9 million, and a total of 35 miles of paved roads spanning a territory the size of France. It was also landlocked, ethnically diverse, and entirely dependent on oil revenue. In other words, it faced every major challenge identified by social scientists as a predictor of state failure. Yet there are American officials who have worked closely on Sudan and South Sudan policy who still feel the situation could have played out differently, and that brutal war could have been avoided. The story of how the South Sudan project came unhinged — pieced together over six months from more than two dozen interviews with current and former U.S., U.N., and South Sudanese officials — is one of extraordinary challenges faced down and enormous errors made by leaders in Juba. It is also the story of how tensions between and within U.S. administrations alienated the South Sudanese government, reduced American leverage, and blinded U.S. officials to warning signs that the new nation’s ruling party was breaking apart. These tensions have come to the fore in the Obama era. Unlike Bush, who one senior White House official told me “could have been the desk officer” because he was so engaged on southern Sudan, Obama has preferred to leave details to his staffers, who have not always seen eye to eye with one another. Key administration posts, including the special envoy to Sudan and South Sudan, ambassador to South Sudan, and assistant secretary of state for African affairs, have remained vacant for extended periods during his presidency. “Through the crucial part of the time that the relationship between [South Sudanese] factions deteriorated, the U.S. had nobody in office,” said John Prendergast, a former Clinton administration official who co-founded the Washington-based Enough Project, a group that works to end genocide around the world.

(Left) Then U.S. President George W. Bush and Salva Kiir meet in the Oval Office on Jan. 5, 2009, in Washington, D.C., to discuss a peace agreement with Khartoum as well as the situation in Darfur. (Right) On Sept. 21, 2011, U.S. President Barack Obama and Kiir, now president of his new nation, pose together for photos at the Waldorf Astoria Hotel in New York City. Credit: Dennis Brack-Pool/Getty Images; Mandel Ngan/AFP/Getty Images There are those who feel that Obama saw little benefit from engaging with the young and troubled nation. Certainly, they say, he did not share the same political incentives as Bush, whose evangelical base championed the southern cause. (The people in the north — present-day Sudan — are generally Arab and Muslim, while the southern population is mostly African and either Christian or animist.) But if ideology and politics mattered, so did personality: Due to a fateful meeting at the United Nations in 2011, at which Kiir reportedly lied to the U.S. president about military action along his country’s northern border, Obama’s relationship with the South Sudanese president was “poisoned from the start,” according to Princeton Lyman, who served as the special envoy to Sudan and South Sudan from 2011 to 2012. The cumulative effect of all these factors was that the United States began to distance itself from South Sudan at a time when the young nation, long supported by Washington, was arguably at its most vulnerable. Without a strong commitment at the highest levels of government, U.S. policy wavered, and relationships between American and South Sudanese officials frayed. Former Obama staffers say that the bulk of U.S. energy was devoted to preventing a return to war between Juba and Khartoum, and that little attention was paid to the dangers that lurked within South Sudan: the gaping internal divisions, dating back decades, that threatened to tear apart the new country’s two most important institutions, the ruling Sudan People’s Liberation Movement (SPLM) and the army. By the time the horrific violence erupted in December 2013, the United States not only proved unable to push the country’s feuding leaders toward a peaceful compromise — it could not reach them for three full days. The importance of America’s role in South Sudan should not be overstated. Secretary of State John Kerry once said that the United States helped “midwife the birth of this new nation,” but while that may be true, the notion that events in Juba reflect the will of Washington policymakers is unfair; a range of factors, both domestic and international, precipitated the civil war and are still shaping its trajectory. Still, most of the sources interviewed for this article felt that the United States had a chance to help South Sudan off its feet — and that it fell down on the job. “Lack of engagement,” Prendergast said, “allowed the thing to go off the rails.”

Hundreds of Christian children – fleeing the civil war between north and south Sudan – reach their ultimate destination of refuge in Palotaka, South Sudan in 1992. Credit: Derek Hudson/Getty Images In the colonial era, successive administrations in Khartoum regarded the lush, swampy south of Sudan as a backwater — when they weren’t plundering it for slaves and ivory, that is. The British suppressed the slave trade in the 19th century, but continued to enrich the center of the country at the expense of the periphery. They undertook a series of major development projects near Khartoum, including what was then the largest irrigation scheme on Earth, but barred southerners from working on them. Even the Foreign Office’s hiring policies reflected its bias: The colonial administration in Khartoum was filled with Oxford and Cambridge graduates, while a less refined corps of military men, widely mocked as the “bog barons,” was dispatched to the south. When independence came in 1956, little changed: In the waning days of its empire, for example, Britain transferred 800 civil service jobs to the Sudanese, but only six went to southerners. This pattern of neglect and exploitation fueled numerous internal rebellions and, ultimately, two civil wars that would split Sudan. The government in Khartoum further alienated southerners by attempting to impose an Arab and Islamic identity on the entire country, a brutal assimilation policy that was dialed up by President Omar al-Bashir, who seized power in a coup in 1989. Bashir embraced the ideology of Hassan al-Turabi, a radical Islamist theologian, and embarked on a revolutionary project that, among other things, involved giving Osama bin Laden a base of operations in the early 1990s. Turabi himself infused the Second Sudanese Civil War with additional religious fervor by indoctrinating new military recruits and sending them to wage jihad in the south. Regional and ethnic differences in the south made consensus difficult to achieve there, a fact that Khartoum manipulated for its own purposes. As with the dramatic 1991 split in the SPLA, referenced by Kiir in his 2013 press conference, many instances of fratricidal conflict occurred after Sudanese intelligence officers armed southerners against each other. In the second civil war, more southerners ultimately died fighting one other than battling Sudanese forces. SPLA soldiers inspect mortar shells on Nov. 13, 1993 in southern Sudan; SPLA soldiers stand with weapons; Colonel John Garang, former SPLA leader poses for a portrait at a rebel encampment in April 1992 near Kapoeta, Sudan; SPLA soldiers with a tank and more artillery on Nov. 13, 1993, in southern Sudan. Credit: Scott Peterson/Liaison Still, despite their inability to put forward a united front, the southerners had fought the Sudanese government to a stalemate by the early 2000s. The 2005 Comprehensive Peace Agreement (CPA), which the United States played a key role in brokering, granted the south partial autonomy and control of 50 percent of Sudan’s oil revenues. It was also supposed to usher in an era of nationwide democratic reforms over a six-year “interim period,” establishing a national “unity” government along with a regional government of Southern Sudan. At the end of the six years, the south would get to decide whether or not it wished to remain a part of Sudan, but the goal was to make secession unattractive. The CPA reflected the vision of John Garang, the leader of the SPLA. But Garang died in a helicopter crash just three weeks after being sworn in as Sudan’s vice president in 2005. The question of whether the south should push for reforms or simply secede from Sudan altogether had always been a divisive one, and Garang’s death dealt a debilitating blow to the reform camp. Without the charismatic rebel commander to lead the way, the interim period quickly became a countdown to a southern independence referendum. By the end of Bush’s tenure in office, analysts were beginning to warn about the possibility of renewed conflict. Garang’s death also vaulted Kiir to the apex of SPLM’s leadership. (The SPLM was the political wing of the independence movement during the second civil war; after 2005, it became a formal political party.) As the interim period progressed, it became clear that Kiir had thrown his lot in with the secessionists. He chose not to challenge Bashir in Sudan’s 2010 national elections and spent little time on issues related to the unity government, according to U.S. officials. He also steered the SPLM toward a strategy of using the United States to force Khartoum to live up to its CPA commitments. “Everything was about getting us to lean on Khartoum,” recalled a former Bush White House official. Almost immediately, there were problems with implementing the CPA: The sharing of oil revenue, security sector reform, and the drawing of new borders between the north and south all proved to be easier said than done. By the end of Bush’s tenure in office, analysts were beginning to warn about the possibility of renewed conflict. In 2007, the SPLM briefly pulled out of the unity government, citing Khartoum’s non-implementation of components of the CPA. Then in 2008, violence erupted between northern and southern forces in the disputed border region of Abyei, displacing as many as 50,000 people. For many Southern Sudanese, the nightmare scenario of Khartoum refusing to allow the independence referendum to go ahead was not difficult to imagine. As noted Sudan activist Eric Reeves wrote in the lead-up to the vote, “Khartoum gives every sign that it is trying to run out the clock, thereby forcing Southern Sudan either to delay the referenda or to make a unilateral declaration of independence.”

Thousands of South Sudanese wave the flag of their new country in Juba on July 9, 2011, to celebrate South Sudan's independence from Sudan. Credit: Roberto Schmidt/AFP/Getty Images A little more than two weeks before he left office, Bush met with Kiir for the last time in the Oval Office. This was the Southern Sudanese leader’s third visit to the White House — an astonishing fact, considering that he was not yet a head of state — and it would be the last meeting Bush would have with any African leader during his presidency. But instead of a sentimental send-off for a man who had done much to advance the southern cause, the meeting was tense and awkward, according to staffers who were present. Kiir, who wore a navy suit, purple tie, and his black cowboy hat, looked agitated and distracted. He let two of his top lieutenants, Foreign Minister Deng Alor and Pagan Amum, the secretary general of the SPLM, do most of the talking. He said almost nothing until the final minutes of the audience, when he made a single, impossible request of the departing U.S. president. “Kiir said, ‘I need you, Mr. President, to say that you will defend South Sudan automatically if the north invades, that the referendum has to go on, and that South Sudan exists under the security umbrella of the United States,” recalled Hudson. “Kiir said, ‘I need you, Mr. President, to say that you will defend South Sudan automatically if the north invades, that the referendum has to go on, and that South Sudan exists under the security umbrella of the United States,” recalled Hudson, who was then the director for African affairs on the National Security Council (NSC). “And Bush just wasn’t going to make that guarantee; he couldn’t make that guarantee.” Kiir had grown increasingly paranoid about a northern plot to derail the referendum, according to former U.S. and South Sudanese officials, and he worried that the United States was not doing enough to ensure that implementation of the CPA proceeded according to schedule. That the Bush administration had turned much of its attention to Darfur, where Khartoum was putting down another insurrection with familiar genocidal zeal, was even more upsetting to the South Sudanese leader. “The way he saw it, any attention to Darfur was attention that wasn’t on them,” said the former Bush White House official. It was against this backdrop that Kiir was seeking a security guarantee from the United States before his most reliable patron was termed out. Sources in the room said that instead, Bush attempted to discuss with the southern leader how Kiir planned to build a new nation after independence. “The president was trying to engage him on what they were doing internally, how they were building their ministries, how they were preparing for the referendum. But he kept just saying, ‘Pagan [Amum] will answer that,’ ‘Deng [Alor] will answer that,’” recalled Hudson. “It was a complete abdication of his responsibility as a leader, something I had never seen in dozens of Oval Office meetings with African heads of state…. Eventually, he offered some platitudes, but it was clear that he hadn’t thought much about this stuff.” Once Kiir had departed, Bush and his team of Africa advisors paused for a moment of reflection. Hudson, his boss Stephen Hadley, the national security advisor, and Jendayi Frazer, assistant secretary of state for African affairs, were all there, as was Richard Williamson, Bush’s envoy to Sudan. “There was a certain nostalgia that the administration was almost over,” said Hudson, adding that they were looking “back on how much had been achieved in Africa and for South Sudan in particular.” Along with nostalgia, however, there was a palpable sense of apprehension. After what Kiir had said in the meeting, according to Hudson, he and his colleagues were thinking to themselves, “Oh, my God, like how the hell are they going to run this place? This is crazy. They have no vision.” Fifteen days later, Obama was sworn in as president. Prior to his election, the junior senator from Illinois had given every indication that he would remain engaged on all of Sudan’s interlocking conflicts. He had co-sponsored the Darfur Peace and Accountability Act, which advocated a more robust multinational peacekeeping force in Darfur, and called for the appointment of a special envoy for Sudan, who would ensure that the CPA was implemented in the south. He had also traveled to refugee camps on the border between Chad and Sudan, where he saw the devastation of the genocide in Darfur up close. “He definitely had a very strong view that he had to stop the dying and killing,” recalled retired Lt. Gen. Scott Gration, who accompanied Obama on the trip and would later serve as his special envoy to Sudan. The two talked a lot about formulating a policy for both Southern Sudan and Darfur while they were in Chad, said Gration, and later also on a trip to Israel. Upon his return to the United States, Obama spoke at a 2006 rally on the National Mall organized by the Save Darfur Coalition, an alliance of advocacy groups working to stop the genocide in the western Sudanese region. His message: “If we care, the world will care. If we act, then the world will follow.” Once in the White House, Obama’s choice of advisors only reinforced the view that Sudan would be a foreign-policy priority. Susan Rice, Obama’s first ambassador to the United Nations, and Gayle Smith, a top aide on the NSC, had been advocating on behalf of the southern Sudanese for years. Vice President Joe Biden and Secretary of State Hillary Clinton, meanwhile, had been hugely outspoken on southern Sudan and Darfur while they were in the Senate. And Samantha Power, director for multilateral affairs on the NSC, had won the Pulitzer Prize for her book A Problem from Hell, which chronicled America’s failure to intervene in genocides throughout the 20th century. By almost any measure, in other words, Obama had assembled a Sudan dream team. In January 2009, the president put Power and Michelle Gavin, his senior director for African affairs on the NSC, in charge of conducting a Sudan policy review. Like most such reviews, the idea was to re-examine the core assumptions of current U.S. policy and ask what exactly the United States wanted to achieve. In addition, Gavin recalled, “We were trying to find a way to manage crises — be responsive to them — without a result that was completely flailing, that was lurching in one direction or another with no sense of the strategic big picture of where you’re trying to get in a year from now and two years from now and five years from now.” Before the team had made much headway, however, it was faced with exactly the kind of crisis the review was supposed to help manage. On March 4, 2009, the International Criminal Court (ICC) charged Bashir with war crimes committed in Darfur and issued a warrant for his arrest. The Sudanese president retaliated by expelling 13 international aid organizations that he accused of having fed information to ICC prosecutors, imperiling between 50 and 70 percent of aid capacity, according to some estimates. “There was a very open tug of war going on that was playing out in the press. There were leaks everywhere. It was a very difficult time to be involved in Sudan policy.” Under pressure to keep the situation from spiraling out of control, Obama appointed a special envoy to Sudan, whose first order of business was getting the aid organizations back up and running. But the man he tapped for the job, Gration, immediately clashed with other members of the Sudan policy review team, and months of infighting began. According to Gavin, Gration had “strong views about how U.S. policy could be most effective” that were “not always shared by other actors around the table.” Hudson, who served as Gration’s chief of staff, was blunter: “There was a very open tug of war going on that was playing out in the press. There were leaks everywhere. It was a very difficult time to be involved in Sudan policy.” The chief fault lines were drawn around how the administration should deal with Khartoum. One camp, which came to be associated with Rice, was in favor of taking a hard line against what it viewed as an irredeemably genocidal regime. The other camp, which formed around Gration, believed that engagement with the Sudanese government was the only way to achieve U.S. objectives in South Sudan and Darfur. “I realized early on that the only path to the referendum and to fixing Darfur led through Khartoum,” Gration told me. “Sure, it would be nice to get the north-south issues … resolved without going to Khartoum, but it wouldn’t happen.” The acrimonious review process dragged on for nine months, during which the United States effectively had no Sudan policy. But the document that eventually came out of it resolved nothing, according to former administration officials. It outlined three uncontroversial and minimally defined objectives — to end the fighting in Darfur, implement the CPA, and ensure that Sudan did not become a haven for terrorists — that contained “the right words for everyone,” as Gration put it. As a result, according to a staffer who worked on the review, fundamental disagreements persisted “even after the strategy was agreed upon,” which, the staffer added, “tells you something about how you could read in your own approach.” By the time it was unveiled, Gration had made it clear that his reading of the policy called for deeper engagement with Khartoum. He made more than 25 trips to Sudan in his first 15 months in office, by his estimation, and threw himself into preparing for national elections in 2010 that were stipulated under the CPA. In his view, the vote offered a “trial run” for the future referendum in the south. To his detractors in the administration, however, Gration’s work amounted to legitimizing Bashir, who was expected to win in a landslide. In the end, the more ideological camp prevailed and Gration was summoned back to Washington. “I got a call from [Tom] Donilon and [Denis] McDonough, saying I’m too close to the election and I got to come back,” the former envoy told me, referring to the then-national security advisor and NSC communications chief, respectively. The message from the White House was clear, Gration said: “We didn’t want to look like we were sanctioning an election that would elect an ICC indictee.” The elections marked the beginning of the end for Gration. The vote was fraudulent and reinforced one-party rule in both the north and the south. The United States muted its criticism so as not to put the upcoming referendum at risk, but behind the scenes, Secretary of State Clinton was losing faith in Gration. Johnnie Carson, the assistant secretary of state for African affairs, recalled Clinton “expressing strong concern” in a morning staff meeting about the “possibility of serious setback on implementation of the most important part of the CPA — the holding of a referendum on South Sudan’s political status.” After that, Carson told me, “I took a hard look at what was going on”; along with colleagues in the State Department’s Africa bureau as well as the envoy’s office, he “put in motion a diplomatic and development surge for the south.”

(Left) A Sudanese supporter of secession pastes posters upon the arrival of Sudan's president, Omar al-Bashir, at Juba airport on Jan. 4, 2010. (Right) A Sudanese man waits outside a polling station in Juba in southern Sudan on April 13, 2010. Credit: Yasuyoshi Chiba/AFP/Getty Images; Roberto Schmidt/AFP/Getty Images The decision was made in the fall of 2010 to beef up the envoy’s office by bringing in Lyman, a former ambassador to Nigeria and South Africa, and Dane Smith, another former ambassador who had served as the special envoy to Liberia in the 1990s. Lyman began running point on southern issues, while Smith advised on Darfur. Clinton and Carson “weren’t too enchanted with Gration, but beyond that they believed that he needed some more help,” Smith told me. With the infusion of new blood into the Sudan envoy’s office, the Obama administration finally began to coalesce around a coherent strategy for getting to January 9, 2011 — the date of the all-important southern referendum. Through what Lyman described as a “long and painful process” led by McDonough at the NSC, officials from the State Department, the envoy’s office, and a host of other agencies hammered out a plan to convince the Sudanese government not to interfere with the referendum and to part with a third of its territory and more than half of its oil reserves if the vote favored independence. (It was a foregone conclusion that this would be the outcome.) Known as the “road map to normalization,” the plan in exchange promised Khartoum sanctions relief and removal from the “state sponsors of terrorism” list. For the Obama administration, the violence presented an additional political problem, since it would be impossible to persuade Congress to lift sanctions on Khartoum, as promised, while Sudan was bombing its own people. The road map was delivered publicly by then-Senator John Kerry — because the U.S. government no longer spoke to Bashir directly after his indictment by the ICC — and bolstered by a diplomatic full-court press that included a high-profile meeting at the United Nations in September 2010, chaired by Obama and attended by other world leaders, in which the U.S. president reiterated the importance of allowing the referendum to proceed. Meanwhile, Lyman, who sources say was effectively in charge of the Southern Sudan portfolio by this point, was working long hours with the southern referendum commission to ensure that it was prepared for the vote. In practice, he said, that meant “countering all the difficult and different things that Sudan threw up as obstacles,” including a lawsuit claiming the referendum was unconstitutional, the withholding of funds to the commission, and even death threats against its chairman. In the end, the referendum went off successfully. Some 3.6 million Southern Sudanese cast their ballots in January 2011 in favor of forming an independent nation, a figure that represented 98.8 percent of the vote. “We have waited 56 years for this day,” Kiir said six months later at the official independence ceremony in Juba. “It is a dream that has come true!” By that point, however, fresh conflicts had already erupted in South Kordofan and Blue Nile, two border regions that remained in Sudan after partition. These areas had been SPLA strongholds during the second civil war, and many residents feared being stranded in a Sudanese rump state that had proved impervious to democratic reforms. For the Obama administration, the violence presented an additional political problem, since it would be impossible to persuade Congress to lift sanctions on Khartoum, as promised, while Sudan was bombing its own people. The result was the demise of the road map, which was added to Khartoum’s long list of perceived betrayals at the hands of the United States. But all was not well, either, in the U.S.-South Sudanese relationship, despite the success of the referendum. The previous 18 months had taken their toll; the internal squabbles that defined the early days of Obama’s presidency had not gone unnoticed in Juba, and South Sudanese officials say they often received conflicting messages from Washington. Amum, the former secretary general of the SPLM, told me, “The Obama administration did not have one policy until after a year, and even after that one year, you find that there still continued to be tension” within the administration. Even more troubling, from Amum’s perspective, was what Gration’s willingness to work with Khartoum said about the U.S-South Sudan relationship. The way he and his southern colleagues saw it, accommodating Bashir meant treating “the question of South Sudan as secondary, as only an element of the relationship between Khartoum and Washington.”

Men queue outside the University of Juba polling center on January 10, 2011, to vote on the second day of South Sudan's landmark independence referendum. Credit: Phil Moore/AFP/Getty Images In the wake of the referendum and the failure of the road map, U.S. officials confronted the reality that almost all critical north-south issues remained unresolved. Borders had yet to be drawn, disputed regions remained, and, most importantly, no agreement had been reached on how to share oil revenues. Lyman, who officially replaced Gration as special envoy in March 2011, estimated that he spent 80 percent of his time dealing with these issues over the next two years. Not infrequently, disputes boiled over into full-blown crises, requiring the U.S. envoy to decamp to Ethiopia for lengthy negotiations led by the African Union and other regional moderators. In January 2012, for instance, a disagreement over how much South Sudan should pay to export its oil through Sudan escalated to the point where Juba shut off the pipeline, eliminating its own most important source of revenue. (Lual Deng, a southerner who served as Sudan’s petroleum minister from 2010 to 2011, told me the decision was akin to “setting fire to your house” instead of securing it after a robbery.) Three months later, the southern army invaded Heglig, a major oil field controlled by Sudan but claimed by both countries, necessitating an eleventh-hour diplomatic push from the United States to get South Sudan to withdraw. Months of negotiations to establish a demilitarized zone between the two countries ensued. Distracted, the United States paid little attention to South Sudan’s domestic political system. Hundreds of millions of dollars of development aid went into various capacity-building programs — financial trainings, instruction in human-resource management, and IT courses, for instance — but former U.S. officials admit that little effort was devoted to helping the SPLM or the army heal their still-gaping internal divisions. “What didn’t happen was that the SPLM became a democratic political movement,” Lyman said. “We didn’t pay enough attention to this.” Amum said he thought the United States was too focused on implementing the CPA and building governance capacity. “That was futile because they were building a body without an engine,” he told me. “The engine was the party, because it is where the ideas are synthesized and where the vision is articulated.” Lyman said he was sympathetic to Amum’s view, but emphasized that efforts to strengthen the SPLM became much more difficult after independence. By law, the United States cannot provide assistance to individual political parties, even when party and government are virtually synonymous, as is the case in South Sudan. Where Lyman does think the United States could have engaged more deeply, and would have been allowed to legally, is in the arena of military cooperation. The United States had a limited military-to-military relationship with South Sudan, relying primarily on contractors to train units and advise on restructuring forces. “We didn’t have officer-to-officer,” Lyman said. “I think, I can’t be sure, that if we had had that relationship, we would have seen the cracks in the military coming. We would have seen the cracks that occurred in December 2013. We might have been able to anticipate it more and do something more about it.” “I think, I can’t be sure, that if we had had that relationship, we would have seen the cracks in the military coming. We would have seen the cracks that occurred in December 2013. We might have been able to anticipate it more and do something more about it.” Again, the Obama administration’s policy reflected internal divisions. “We had a difference in the administration over [whether] you establish a strong military presence,” Lyman said. Some officials worried that Khartoum might misinterpret a more robust U.S. presence in the south. Others worried about lack of housing and staff in Juba. “We debated that. Africom came in and did 12 studies or something like that [but] we never resolved it," he said, referring to the United States Africa Command. I asked Majak D’Agoot, who served as Kiir’s deputy defense minister during this period, what he thought of his country's military relationship with the United States. “I was a little bit concerned about the role of contractors, because contractors don’t carry any political influence and people don’t trust contractors,” he said. “Contractors cannot talk to us about issues of the military being apolitical, nonpartisan, this kind of thing. But when we deal with U.S. officers, they will be transferring traditions to us and those traditions will have long-lasting influence on the South Sudanese military into the future.” These missed opportunities were compounded, sources say, by another serious problem that reduced American influence in South Sudan: the souring of relations between Kiir and Obama. Sources close to Kiir say that, perhaps because he enjoyed such a close relationship with Bush, he has always felt slighted by Obama. Andrew Natsios, who served as Bush’s special envoy to Sudan from 2006 to 2007 and has remained in contact with Kiir, told me the South Sudanese president complained to him that Obama “didn’t engage him. He didn’t treat him like a head of state.” The U.S. president has never invited Kiir to the Oval Office, and the pair’s first meeting came at the United Nations in September 2011 — two months after Kiir had become an official head of state, and more than two and a half years into Obama’s presidency. Things did not go well at the meeting, either. One of the thorniest issues U.S. diplomats had to deal with in the post-independence period was South Sudan’s continued support for rebels who were left north of the country’s border after partition. These fighters from the SPLM–North, as the group is known, had battled Khartoum alongside the southerners for decades, so Juba’s decision to back them covertly when violence broke out in Blue Nile and South Kordofan in 2011 came as no surprise. Yet proxy warfare turned up the heat in the already fraught north-south relationship, and U.S. officials worried it could herald a return to open conflict. After months of denials from the South Sudanese about backing the rebels, Obama used his first face-to-face meeting with Kiir to confront the new president with satellite evidence. In the lead-up to the meeting, U.S. officials reached out to the South Sudanese delegation and zeroed in on the importance of building trust between the two governments: If Kiir wasn’t prepared to acknowledge the covert actions of his military, the officials said, he should at least tell Obama he was looking into the matter. But when Obama raised the issue at the tail end of the meeting, Kiir responded by suggesting the United States check the accuracy of its satellites. “I tell you, I almost fell off my chair,” Lyman told me. “All of us on the American side, we couldn’t believe it.” That evening, Susan Rice laid into Kiir, according to sources with knowledge of the exchange, and sometime later, a letter arrived from the South Sudanese president alluding vaguely to “new information” about the fighting across the border in Sudan. But when Lyman and McDonough, by then the deputy national security advisor, brought up the correspondence during a subsequent meeting in Juba, Kiir feigned ignorance. “What letter? What new information?” he asked, according to Lyman. “We don’t help them in South Kordofan or Blue Nile.” “Denis was so angry,” the former envoy recalled. “Having lost Obama, [Kiir] then lost Denis McDonough.” One year later, in December 2012, Lyman penned his letter of resignation. The U.S. president requested that he stay on until a successor could be found, but after three months without a replacement — during which the former special envoy said he was considered a “lame duck” in Juba — he stepped down of his own accord. A week later, on March 29, Carson, the assistant secretary of state for African Affairs, submitted his own resignation. The White House did not replace either of them until August of that year, leaving two critical posts vacant during what would prove to be the most decisive period in South Sudan’s brief independent history.

Several South Sudanese shelter at a makeshift IDP camp at the United Nations Mission in South Sudan (UNMISS) compound in Juba on Dec. 22, 2013. People fled there amid fears that fighting would resume in the capital. Credit: Tony Karumba/AFP/Getty Images Relations between Kiir and Machar had always been tense, but in March and April 2013 they became openly hostile, as the ambitious vice president prepared to challenge his boss for the SPLM chairmanship, a post that would all but guarantee victory in the next presidential election. “I think that was the breaking point,” said Lam Akol, the former Sudanese foreign minister, who now leads a small opposition party in Juba. Kiir countered by delaying the party convention where the vote on the chairmanship was due to take place and by withdrawing powers he had delegated to Machar. With his path to the presidency seemingly blocked, the disgruntled vice president began to hint at the possibility of violence. Akshaya Kumar, a Sudan and South Sudan policy analyst with the Enough Project, met with Machar that May. She recalled him saying ominously, “The president should know that the army is 80 percent Nuer.” The following month, Kiir dismissed two ministers who had spoken out against him. Not long after that, he fired the governor of Unity, Machar’s home state, who was thought to be loyal to the vice president. Then, on July 23, the president delivered his coup de grâce: He sacked his entire cabinet, including Machar, and replaced its members with a combination of loyalists and technocrats. Machar fired back with a renewal of his pledge to challenge Kiir for the presidency, telling the press, “If [the country] is going to be united, it cannot tolerate one man’s rule. It cannot tolerate dictatorship. It cannot tolerate tyranny.” Improbably, nothing happened for four months. But Kiir’s apparent triumph over his rivals proved to be the calm before the storm. The early days of December 2013 brought with them a number of ominous signals, including a press conference by a lengthy cast of political discontents, including Machar, Amum, and Rebecca Nyandeng De Mabior, the wife of John Garang. The media were ordered not to cover the event, but word of the officials’ incendiary remarks criticizing Kiir was soon buzzing around the capital in the lead-up to the long-delayed meeting of the SPLM’s top legislative body, the National Liberation Council (NLC). By that gathering, finally held on December 14, there appeared to be little hope of de-escalating the situation. According to Kosti Manibe, who had been removed from his post as finance minister in June 2013 but attended the meeting as a party official, Kiir positioned armed guards inside the convention center where the event was being held as a show of force. After a contentious first day, in which Machar’s allies tried and failed to pass legislation making it easier to contest Kiir for leadership of the SPLM, a number of officials, including Manibe, decided to boycott the remainder of the proceedings. “Many of us who were later arrested thought it didn’t make any sense to attend,” the former finance minister told me when I visited him in Nairobi, where he is living in exile. “It was a waste of time. We did other things. It was a Sunday. I personally sat in my house all day.” That night, a firefight broke out between Dinka and Nuer members of the Presidential Guard, an elite military force that answers directly to the president. Before long, the NLC boycott was being spun as evidence of a plot to overthrow the government, and the following day, Manibe was arrested along with a number of other politicians who had spoken out against Kiir. As Juba descended into chaos, sources say the United States found itself completely in the dark. The new special envoy, Donald Booth, had been in office since August, but neither he nor Ambassador Susan Page was able to reach Kiir for the first three days of the crisis. “I was the first to get through to him,” Booth told me. “We were not able to reach him by phone” until two days after Kiir’s threatening news conference on December 16. By then, hundreds of people had been killed in ethnic massacres in Juba and the government had lost control of Bor, the capital of Jonglei state. South Sudanese troops loyal to President Salva Kiir at Bor airport, which has been recaptured from rebel forces; A body, reportedly that of a rebel, lies on the ground in the market in the center of Bor, on Dec. 25, 2013; SPLA soldiers talk at Bor airport. Credit: Samir Bor/AFP/Getty Images; Waakhe Simon Wudu/AFP/Getty Images; Samir Bol/AFP/Getty Images Booth, a former ambassador to Ethiopia, had tried to talk the parties off the ledge in early December. As tensions flared over the NLC meeting, he met with both Kiir and Machar in Juba and cautioned the parties against doing “anything that would burn down their house.” “Obviously, they didn’t listen,” he told me. Once the violence erupted, the Obama administration scrambled to find someone with enough cachet in Juba to corral the feuding leaders. Former presidents Jimmy Carter and George W. Bush, as well as former Secretary of State Condoleezza Rice, were enlisted to reach out to Kiir and Machar. Even Pope Francis sent a Christmas message at Obama’s request. “We were really trying to find anybody who could get through to these guys who had miscalculated very badly and plunged their country into war,” Booth said. The all-hands-on-deck approach may have been Obama’s best bet under the circumstances, but it also underscored the extent to which the administration had fallen short of the goal articulated by Gavin way back at the beginning of the Sudan policy review in 2009: Crisis management had become the strategic goal. Relying on officials from former U.S. administrations also risked being seen as the desperate flailing of a White House that had long ago lost the ear of Kiir’s regime. As D’Agoot, the former deputy defense minister, told me, “The rapport between [Kiir] and president Obama is not good, so the U.S. administration decided on employing that alternative channel to make the message sing.” Unfortunately, the message fell flat despite the messenger. Booth’s office managed to negotiate the release of some political prisoners — including Amum, Manibe, and D’Agoot — and to wrangle a string of cease-fire agreements, but those were often dead-letter in a matter of hours. As it became clear that the two sides were determined to slug it out on the battlefield, the Obama administration resisted upping the diplomatic ante. Conspicuously absent from the on-again-off-again peace talks that began in Addis Ababa in early 2014 was Secretary of State Kerry, who was then consumed by his bid for Middle East peace. Some critics have suggested that Kerry steered clear of South Sudan for political reasons. “There was a sense that the State Department didn’t want to use Kerry until he could deliver some kind of victory,” said Hudson. “In retrospect, there’s a belief that the administration waited way, way too long to use him in a really public way.” A spokesperson for the secretary of state did not respond to multiple requests for comment. When he has since been engaged, sources say Kerry has gotten modest but real results. After his one and only trip to the region since the fighting in South Sudan began, in May 2014, the parties agreed to form a transitional government, the details of which they have been ostensibly negotiating ever since. “It was not a coincidence that the agreement followed Kerry’s visit,” said Prendergast. “As soon as he shows up in Addis, boom, things start happening.” Then, in August, when nearly 50 African heads of state were in Washington for the U.S.-Africa Leaders Summit, the secretary of state played an important role in convincing regional powers, including Kenya, Ethiopia, and Eritrea, to present a unified front at the peace talks in Addis. But Kerry’s involvement has been sporadic, and the peace process has dragged on for months without putting an end to the civil war. To date, seven cease-fire agreements have broken down, leading many observers to doubt the sincerity of the negotiators. “The motivations of those that triggered the conflict are such that they don’t care about the suffering,” the United Nations high commissioner for refugees, former Portuguese Prime Minister António Guterres, told me in September. He added that after previous peace agreements, both parties “went on as if nothing has happened.”

Displaced people carry water as they walk through a security corridor at the entrance of a U.N. base in Malakal on Feb. 6, 2014. Credit: Carl De Souza/AFP/Getty Images When I went to see South Sudan’s foreign minister, Barnaba Marial Benjamin, in September, international outrage over the slow pace of negotiations had hit a fever pitch. The U.N. Security Council had just sent a delegation to Juba to threaten sanctions, and Kerry and Rice, now Obama’s national security advisor, had each issued strongly worded statements blaming the government and the rebels in equal measure for the ongoing violence. “Deadlines keep passing and innocent people keep dying,” Kerry said in a statement in August. “This is an outrage and an insult to the people of South Sudan.” I asked Marial if he was surprised by such tough remarks. “Not only was I surprised, but I think that it was unfair to hold both parties responsible,” he told me, his voice elevated to register dismay. The rebels “have been the ones violating the cessation of hostilities,” whereas the government “has not moved an inch forward to any other territory controlled by the rebels,” he said. (Reports by regional monitors deployed to observe the cease-fires have since blamed both parties for violating the truces.) The foreign minister went on to emphasize that Kiir’s government is democratically elected, and that merely agreeing to peace talks was a significant concession on the part of the president. “The fact that we agreed to talk to a rebel group that attempted to change the government — an elected constitutional government — through the use of force is a great signal on the side of the government,” Marial said. “There is no elected government anywhere in the world that can do that. But the government of South Sudan has done that.” “Imagine the first American pioneers, when they went to the United States, they found it bush and wild and shooting out. They had to put all their effort to build it what it is,” Marial told me. “That’s why we say that what South Sudan needs is understanding and help, not punishment.” Marial then turned to the American frontier to bolster his case: Why was the United States intent on punishing South Sudan, he wondered, when the African nation was “beginning from scratch” just as the first colonists had when they landed at Plymouth? “Imagine the first American pioneers, when they went to the United States, they found it bush and wild and shooting out. They had to put all their effort to build it what it is,” he told me. “That’s why we say that what South Sudan needs is understanding and help, not punishment.” (He isn’t the only who’s made such comparisons: Amum had suggested looking to the Continental Congress for insight into South Sudan’s political development when I interviewed him in Nairobi.) As much as South Sudanese officials feel collectively aggrieved by the Obama administration’s cold shoulder, the United States has not totally abandoned Kiir. Despite his government’s growing authoritarianism and mounting evidence of war crimes committed by the SPLA, Washington has refrained from sanctioning South Sudanese political leaders — though it has slapped two military commanders on either side of the conflict with asset freezes and travel bans — and has shielded the country from a U.N. arms embargo. A draft sanctions resolution reportedly languished for months at the United Nations because of disagreements between the United States and European nations over whether to ban the sale of weapons to Kiir’s government. It was finally circulated in January without reference to an embargo. Booth told me in December that the United States doesn’t want to “box in the negotiations” with additional punitive measures before regional powers like Ethiopia and Kenya have signed off on them. “You need to have the regional cooperation, or else you’re going to have just another hollow sanction,” he said. “So we’re working to get the region on board with anything we’re able to do in New York.” Just how closely South Sudanese officials are watching events in Turtle Bay was driven home by a last-minute charm offensive by Marial in December, when rumors about the possible U.N. sanctions package appeared in the press. The South Sudanese foreign minister flew to Washington to reassure U.S. officials that the peace talks in Addis Ababa were in fact making progress. “It’s just like you’re running a marathon, and you’re just 10 meters away” from the finish line, Marial told reporters. “We need assistance. We need help, not punishment.” A little more than two weeks later, the negotiations collapsed once again. They were resuscitated in January, and in early February, the parties recommitted to a cease-fire and agreed in principle to form a transitional government by March 5, with Kiir as president and Machar as vice president. In other words, they wound up right back where they started. The details of the power-sharing deal have yet to be worked out, however, and fighting has already resumed on the battlefield.

SPLA soldiers wave their AK-47s in the air as they celebrate alongside IDPs outside the UNMISS base in Malakal after the SPLA claimed it had recaptured the town from rebels on March 19, 2014. Credit: Ivan Lieman/AFP/Getty Images) When I visited the U.N. base in Malakal, many people forced from their homes by the war had already stopped waiting for updates from Addis Ababa. At the time, displaced civilians were crammed into so-called “protection of civilians” sites (POCs), where rainwater mixed with human excrement and flowed freely among makeshift tarpaulin dwellings. The U.N. was in the process of moving people to slightly higher ground, but funding shortfalls, coupled with the high cost of backfilling swampland to build on, meant that thousands of people were still living below the waterline. “The situation is not one in which you can look to the future,” said Emanuel Wol, a former Health Ministry employee who now works as a translator for international NGOs. “I’m scared to hear the radio.” “Even as we were swimming through the water, the bullets were chasing us.” A soft-spoken man with gap teeth and an infectious smile, Wol was at home when rebel forces swept into Malakal in February 2014. He had sent his family north to Khartoum after the initial wave of attacks, but elected to stay behind in order to keep watch over their belongings. When the shooting started, most people ran for the U.N. base, but Wol was afraid he was too far away to make it in time. Instead, he raced for the Nile River, where he recalled being caught in a stampede of deserting soldiers and terrified civilians. “The rebels were shooting the soldiers, but they were among us,” he told me. “Even as we were swimming through the water, the bullets were chasing us.” Wol survived by swimming and wading six miles downstream to a settlement called Wau Shilluk. By August, when we met, he was trying to leave the base as infrequently as possible. With rebels and the SPLA shelling each other across the Sobat, a Nile tributary located some 20 miles to the south, any trip to the outside world carried with it the risk of being stranded in the midst of an attack. Even fetching water or food rations within the POCs could be dangerous, given the ever-present threat of sexual assault or ethnically motivated violence. “The ethnic tensions on the inside mirror the ethnic tensions on the outside,” said Deborah Schein, the coordinator for the U.N. mission in Upper Nile state, where Malakal is located. On several occasions, deadly clashes had erupted between communities inside the camps.