South Sudanese Civil War
|South Sudanese Civil War|
|Part of Ethnic violence in South Sudan[dubious ]|
Map of South Sudan
Nuer White Army
|Commanders and leaders|
| Salva Kiir Mayardit
Paul Malong Awan
Kuol Manyang Juuk
James Hoth Mai (until 2014)
| Riek Machar
Nuer White Army: 25,000
|Casualties and losses|
It began on the evening of 15 December 2013, at the meeting of the National Liberation Council meeting at Nyakuron, when opposition leaders Dr. Riek Machar, Pagan Amum and Rebecca Nyandeng voted to boycott the Sunday December 15, 2013 meeting of the National Liberation Council (NLC). President Salva Kiir ordered the Sudan People’s Liberation Movement (SPLM) Major General Marial Ciennoung, commander of the Presidential Guard (The Tiger Battalion) to leave the meeting venue and return to the barracks to disarm the troops. After disarming all ethnicities within the guard, Marial allegedly ordered that the Dinka members be re-armed. His deputy, from the Nuer ethnicity, began to question this order and a fight ensued when surrounding officers saw the commotion. The Nuer soldiers also re-armed themselves. Fighting erupted between the Dinka elements of the Presidential Guard and the Nuer elements, lasting from Sunday night until Monday afternoon. Civilian casualties began when the Dinka elements of the SPLM began targeting Nuer civilians in the capital city of Juba.
President Salva Kiir has called it a coup attempt and announced that it had been put down the next day, but fighting again erupted on 16 December and spread beyond the capital, Juba, to the region around Jonglei which is prone to ethnic conflict. Early estimates stated that at least 1,000 people were reported to have been killed and over 800 other people were injured  in Juba, but this number has now been cited to be much higher than initially thought as a Human Rights Watch article cites eyewitness accounts of large numbers of bodies on December 17, and their removal in trucks to an undisclosed location December 18. Eyewitness accounts also cite SPLM Dinka troops assisted by guides in house to house searches to Nuer homes and killing civilians in Juba. Similar door to door searches of members of the Nuer ethnicity have been reported in the government held capital city of the Upper Nile State, Malakal. A final death toll of civilian casualties in government held cities of Juba, Malakal, and Bentiu has not been released. The International Crisis Group estimated in their April 2014 report that over 10,000 had been killed in the conflict.
Kiir blamed former Vice President Riek Machar for instigating the "coup" but no evidence of a coup attempt has been found. Former Vice President Riek Machar has denied a coup attempt and instead blamed Kiir for playing power politics. Bor was seized by a Nuer militia on 19 December. On the same day, a UN compound was stormed in Akobo, Jonglei, resulting in the deaths of two Indian UNMISS peacekeepers. The UN Secretary General expressed deep concern as UN staff received threats from the body guards of Senior government Information Minister that demanded armed access to UN Mission Camps where civilians are sheltering. Following this incident President Salva Kiir accused the UN of sheltering armed opposition forces in their UN Mission, which the UN denied. Salva Kiir also accused the UN of an attempted take over of his leadership.
- 1 Background
- 2 Course of the conflict
- 3 Massacres of civilians
- 4 Casualties
- 5 See also
- 6 References
- 7 External links
President consolidates power
After rumors about a planned coup surfaced in Juba in late 2012, South Sudanese President Salva Kiir began reorganizing the senior leadership of his government, party and military in an unprecedented scale. In January 2013 Kiir replaced the inspector general of the national police service with a lieutenant from the army, and dismissed six deputy chiefs of staff and 29 major generals in the army. In February 2013 Kiir retired an additional 117 army generals but this was viewed as troublesome in regards to a power grab by others. Kiir had also suggested that his rivals were trying to revive the rifts that had provoked infighting in the 1990s.
In July 2013, Kiir dismissed Vice President Riek Machar, one-time leader of the Nasir revolt, along with his entire cabinet. Kiir suspended the SPLM Secretary-General Pagan Amum Okech and forbade him from leaving Juba or speaking to the media. The decrees elicited fears of political unrest, with Machar claiming that Kiir's move was a step towards dictatorship and announcing that he would challenge Kiir in the 2015 presidential election. He said that if the country is to be united, it cannot tolerate "one man's rule."
Kiir disbanded all of the top-level organs of the SPLM party, including the Political Bureau, the National Convention and the National Liberation Council in November 2013. He cited their failed performance and the expiration of their term limits.
Although Machar and Kiir are both members of the SPLM, they stem from different tribes with a history of conflict. Kiir is an ethnic Dinka, while Machar is an ethnic Nuer. Some observers reject ethno-tribal explanations of the conflict as overly simplified.
Course of the conflict
The South Sudanese Sudan Tribune reported clashes breaking out in the Munuki neighbourhood late on 14 December in South Sudan's capital, Juba, between members of the presidential guard. Kiir also claimed that the fighting began when unidentified uniformed personnel started shooting at a meeting of the SPLM. Former Minister of Higher Education Peter Adwok said that on the evening 15 December after the meeting of the National Liberation Council had failed, Kiir told Major General Marial Ciennoung to disarm his soldiers of the "Tiger Battalion," which he did. Adwok then controversially claims that the officer in charge of the weapons stores, opened them and rearmed only the Dinka soldiers. A Nuer soldier passing by questioned this and a fistfight then ensued between the two and attracted the attention of the "commander and his deputy to the scene." Unable to calm the situation, more soldiers got involved and raided the stores. It culminated in the Nuer soldiers taking control of the military headquarters. The next morning, he says that Sudan People's Liberation Army (SPLA) reinforcements arrived and dislodged the mutineers. He then explained standard procedure:
Military doctrine dictates that once a contingent of mutinous troops have been dislodged, appeal is made for their surrender and then disarmed. Those who remained loyal (to the president) are also disarmed to prevent bad blood. The loyal troops of Tiger, hailing mainly from Warrap and Aweil, have not been disarmed. In fact, they are the ones rampaging Juba, looting and shooting to kill any Nuer in the residential neighbourhoods."
Adwok was then placed on a list of wanted politicians, to which he said "this may be my last contribution, because, as I said, I'm waiting for the police in order to join my colleagues in detention." On Christmas Day,five days after his controversial publication, Adwok was arrested and held for two days. He was later detained at the Juba airport when attempting to leave the country. His passport was also confiscated.
The military headquarters near Juba University was then attacked with fighting continuing throughout the night. The next day heavy gunfire and mortar fire were reported, and  UNMISS announced that hundreds of civilians sought refuge inside its facilities Aguer said that some military installations had been attacked but that "the army is in full control of Juba," that the tense situation was unlikely to deteriorate, and an investigation was under way. Several people were also injured during the fighting. Juba International Airport was closed indefinitely; Kenyan airlines Fly540 and Kenya Airways indefinitely suspended flights to Juba after the airport closed. A dusk-to-dawn curfew was imposed until further notice. State-owned SSTV went off-air for several hours. When it returned to broadcasting, it aired a message by President Salva Kiir. The dissident group was said to include Sudan People's Liberation Movement (SPLM) founder John Garang's widow, Rebecca Garang.
Foreign Minister Barnaba Marial Benjamin said that soldiers at the army base attempted to raid a weapons store but were repulsed. He added that unnamed politicians had also been arrested, but could not confirm if Machar was one of them. He also said that those that were a part of the coup were "disgruntled" soldiers and politicians led by Machar. At least ten people were confirmed to have been detained, including former Finance Minister Kosti Manibe. Five others were sought for questioning, including Machar and Pagan Amum. Information Minister Micheal Makuei Leuth claimed that Machar had left Juba with some soldiers and stolen cattle. Of those arrested, seven were confirmed as former ministers. Other arrests included those of Kiir's critics. Amum then said on 15 December that "I am fine, that's all I can say," while Machar announced through his spokesman, James Gatdet Dak, that he had not been arrested and was doing well. However, it was later reported that Amum was being held by the state security apparatus.
President Salva Kiir spoke on national television on 16 December, having abandoned his traditional suit and cowboy hat for military fatigues, and said, while surrounded by government officials, that the coup had been foiled and that it was orchestrated by
a group of soldiers allied with the former vice president. The attackers went and (the) armed forces are pursuing them. I promise you today that justice will prevail.
Your government led by the SPLM has articulated the ideals of democracy in the party as well as in the government, and I will never deviate from them at any cost. The SPLM is fully committed to the peaceful and democratic transfer of power, and will never allow political power to be transferred through violence.
Kiir said that the government was then "in full control of the military situation" and that those "criminals" responsible for the attack would be brought to justice. On 21 December, the government announced on Twitter its unconditional readiness to hold peace talks with any rebel group, including Dr. Riek Machar  Kiir spoke in a Christmas message that "innocent people have been wantonly killed. There are now people who are targeting others because of their tribal affiliation...It will only lead to one thing and that is to turn this new nation into chaos."
Machar spoke for the first time since the crisis began on 18 December in which he said he was not aware of any coup attempt, but instead blamed Kiir for fabricating such allegations of a coup in order to settle political scores and target political opponents. He also said the violence was started by the presidential guard, which was founded by Kiir and told to report directly to him instead of the military. He added: "My bodyguards at the vice presidential residence were summarily executed. They attacked it with tank shells and then burned. It is rubble now. They fired on my residence and I fled. My life was in danger; my colleagues were being arrested for no reason. They are not plotters, it was not a coup. Nobody wants that." Instead, Machar maintained that Kiir "used [Machar] as a scapegoat" to enable him to purge the SPLM of his rivals and avoid reforming it. He also commented that "the violence is turning tribal and they are killing people in Juba," depicting the people in Jonglei rising up to take on the majority Dinka. "Some really heart-wrenching acts have already occurred where Nuer soldiers have been attacked and killed, Nuer government officials, even those serving in the offices of Nuer ministers, and ordinary citizens suspected of having participated in the fight against the government. [At Nairobi Jomo Kenyatta airport, those who have fled speak of] door-to-door executions of Nuer. [Kiir is] inciting ethnic killings and tribal divisions, [he is no longer South Sudan's] legitimate leader. [He] is covering for his inefficiency in running the government and the army." He refused to deny or acknowledge support for Gadet but that "the rebels are acting in the right direction." On 22 December, Machar said he wanted to be the leader of the country and that "his" forces would maintain control of the country's oil fields.
Chief Whip and MP from Eastern Equatoria Tulio Odongi Ayahu called for dialogue and warned that the Equatoria region would not be a participant in the conflict after holding talks with Vice President James Wani Igga. "We Equatorians will promote dialogue. We will not accept undemocratic methods to come into power. At present there is a leader in place. And this leader will have to complete his term of office. Those who may be thinking to take over power by means of violence will not be accepted by the Equatorians. [The opposition is making] premature challenges towards the elected president" and should have used the SPLM party convention and congresses in 2014 instead of "circumvent[ing] the procedure."
Jok Madut Jok wrote: "If the SPLA engages Gadet and possibly Riek and Taban, then we have an all-out civil war in South Sudan, a mere two years after independence, and making good all the predictions by outsiders that South Sudanese will have limited capacity to build a peaceful nation" and "sounds of gunfight, traversed with heart-shaking mortar and tank blasts, and which have continued sporadically well into today Wednesday morning, have all spread fear in the population, leaving them hostage to the madness of a few power-hungry men...[the uncertainty centres on] the fate of political stability in the whole country."
The SPLM-affiliated youth group condemned the attempted overthrow of Kiir and a statement read: "We the SPLM-concerned youth group rejects in totality the notion and culture of using violence as a means to attain, retain or transfer power. The conflict is not between the Dinka and Nuer, but between government and those who lost power in the July reshuffle. We urge security forces to act with restrain in order to avoid the conflict from taking an ethnic dimension".
Beginning of rebellion
Despite government claims of having quashed the alleged coup, a further centre of fighting erupted on 17 December round Bor, in Jonglei, where three people had died; and over 1,000 people sought refuge in the UN base. Fighting started again at 9:00 from a military headquarters and another military barrack, according to Hussein Maar, deputy governor of Jonglei. Fighting also occurred near the presidential palace and other areas of Juba. Ajak Bullen, a doctor at a military hospital, said that "so far, we have lost seven soldiers who died while they were waiting for medical attention and a further 59 who were killed outside." The Juba Teaching Hospital had previously confirmed 26 deaths – the same number as the government – but there was no confirmation of overlap or which side the dead soldiers were fighting for. Hospital director Ajak Bullen said that 400 people were being treated. The International Crisis Group (ICG) also reported that some fighting occurred between the Dinka and Nuer in Pibor in Jonglei amid reports of ethnically targeted killings. It also reported that Machar's house had been bombarded and "surrounded, including with tanks", while "parts of Juba have been reduced to rubble" and that fighting between Nuer and Dinka had taken place at military barracks in Jonglei. Communication links were either down or poor. The local Radio Tamazuj suggested UNMISS were absent from the streets in Juba during the early fighting and that December 2013's president of the UN Security Council, France's Gérard Araud, had announced that the UN peacekeepers would not intervene in the fighting. Amongst NGOs, Emma Jane Drew, the acting director of Oxfam's South Sudan office, said in the first days of the conflict that her team were unable to leave their compound in Juba because of "continued shooting."
Fighting between military factions later erupted beyond Juba in Jonglei, amid fears of a wider conflict. Aguer said that there was overnight fighting among troops in Jonglei on 17–18 December and that he was verifying reports of desertions from the military. This followed reports from the ICG that Nuer in the area were defecting from the armed forces and that the Dinka people feared a repeat of the 1991 massacre by the Nuers. Meanwhile, in Juba, a semblance of calm had returned by 18 December with a trickle of traffic. The UN reported that 13,000 people were taking refuge from the fighting in its two compounds in Juba.
On 19 December, a Nuer militia led by Peter Gadet, the defected former 8th Division commander, claimed control of Bor, while Aguer said: "Our soldiers have lost control of Bor to the force of Riek Machar late on Wednesday. There was shooting last night. We don't have information on casualties or the displaced in the town, as operations are ongoing." It came a day after Kiir said he was willing to have talks with Machar. Ethnically targeted violence was also reported.
Nuer fighters overran the UN base in Akobo, Jonglei, in pursuit of civilians who had sought refuge there. Violence in Juba reportedly calmed, though there were unconfirmed reports of several students killed by security personal at Juba University on 18 December. The UN announced that thousands of people had sought refuge within the UN's compounds The Indian Ambassador to South Sudan Asoke Mukerji had originally said that three Indian peacekeepers were killed, but UNMISS later said that one of them was only injured and then evacuated to a UN medical facility in Malakal. Special Representative of the UN Secretary-General Hilde Frafjord Johnson noted that the two killed Indian soldiers were helping to protect 36 civilians, when they were attacked by about 2,000 armed youths. “(The youths) opened fire and attacked... from all directions... with the apparent intention of killing the civilians taking shelter there,” Ms. Johnson said. The attack had also resulted in loss of contact with the base while Farhan Haq said the fate of over 30 ethnic Dinka civilians at the base was not known. In response to the incident UN Secretary-General Ban Ki-moon issued a statement that read he was "appalled" to learn of the incident and that "there are indications that civilians may have been killed and wounded in the attack, but this remains to be verified. Should these reports prove true, those responsible must be held accountable for their crimes."
At the same time, about 200 employees of the regional petroleum operators, of which the three largest were China National Petroleum Corp, ONGC Videsh and Petronas, sought refuge at an UN compound in Bentiu, Unity State. UNMISS spokesman Joe Contreras said: "We expect their presence to be temporary because we understand that the company they are working for will be arranging for transport to get out of Unity State." Leuth said that the petroleum producing areas have not been affected by the conflict. This followed the deaths of 16 such workers, five workers at a field in Unity State on 18 December and another 11 at the Thar Jath field the next day. Government soldiers then took control of the fields and said that production continued normally. Unity Governor Mabek Lang De Mading said on 18 December: "We have sent reinforcements to Unity yesterday night and they contained the situation. This morning fighting broke out in Thar Jath. We have sent reinforcements and they have now contained the situation. It is stable now." The rebels had reportedly taken over at least some of the country's oil fields amidst fears of Sudan intervening in the country.
Mutineers clashed with troops loyal to President Kiir inside the barracks of the SPLA 4th Division in Bentiu, the capital of Unity State since the evening of 20 December. Heavy fighting over the night resulted in the retreat of the loyal forces from the barracks.
On the morning of 21 December, Maj. Gen. James Koang Chuol, commander of the SPLA's 4th Division, announced on the radio that he had defected and had removed Unity State's governor. He said he had formed a new interim administration and urged people to return to work and remain calm. Juba confirmed that it lost control of Bentiu to a commander loyal to Machar, although Machar denied this.
Forces loyal to the government of South Sudan have moved from Bentiu to the outlying Abiemnom County after the defection of much of the SPLA 4th Division along with its commander. They were later reinforced by SPLA troops from Western Bahr el Ghazal’s 5th division and from Northern Bahr el Ghazal’s 3rd division.
In the north of Unity, Pariang county is home to the Rueng Dinka —the only Dinka group in the state. Fighting broke out in Pariang on 20 December, when some SPLA troops defected to the rebels. On 24 December, an estimated 400 defectors moved southwards from Jaw, the SPLA’s northernmost operating base towards positions held by SPLA forces loyal to Koang Chuol. As of 26 December, the SPLA claimed they had destroyed 37 rebel vehicles in Pariang county, which remains in the hands of the SPLA.
On the same day the ‘interim government’ of the former SPLA 4th Division Commander James Koang in Unity State announced itself loyal to the former vice president of the country, for the first time openly declaring support to the opposition leader. In an interview on 26 December, the spokesman of the self-declared interim government of the state says that they are now under the direction of Dr. Riek Machar.
Following calls from the government of South Sudan, Uganda deployed its troops to Juba to assist in securing the airport and evacuating Ugandan citizens. On 21 December a flight of three US Air Force V-22 Osprey aircraft en route to evacuate US nationals from Bor took small arms fire from the ground, injuring four Djibouti-based Navy SEALs on the ground security team. The Ospreys aborted, diverting to Entebbe International Airport from where the wounded personnel were flown on to Nairobi, Kenya, for medical treatment. South Sudan blamed the rebels for the incident. An estimated 743,400 people are displaced within South Sudan. Another 130,400 people have fled to neighboring countries.
A second evacuation attempt by four UN and civilian helicopters succeeded in evacuating about 15 US nationals, Sudanese-Americans and those working in humanitarian operations, from the United Nations base in Bor on 22 December. Although the base was surrounded by 2,000 armed youths, a rebel commander had promised safe passage for the evacuation. In total 380 officials and private citizens as well as about 300 foreign citizens were flown to Nairobi. Over 800,000 people have been displaced inside South Sudan, while almost 255,000 have fled as refugees to neighboring countries of Ethiopia, Kenya, Uganda and Sudan, the U.N. said.
On 22 December, a full-scale tank battle erupted between defected and loyalist factions in Upper Nile. At the same time, U.S. and Nigerian envoys were on their way to Juba to try to negotiate a solution.
In an escalation of the conflict, Aguer said on 23 December that "the army is on its way to Jonglei and Unity to retake territory and will attack within a few hours." This followed the U.S. envoy to the country, Donald Booth, saying that having spoken to Kiir, the latter was committed to talks with Machar without preconditions. The United States military also announced a repositioning of its forces in Africa to prepare for possible further evacuations as the United Nations warned of the planned strikes. At the same time, despite the offer of talks, South Sudan Information Minister Michael Makuei said that "there is no way we will release anybody who is accused of a coup d'état," and he dismissed claims by Machar that rebels had taken over all the major oil fields in Unity and Upper Nile as merely "wishful thinking." It came after Machar said he had spoken to U.S. National Security Adviser Susan Rice and U.N. envoy Hilde Johnson about resolving the conflict. "My message was let Salva Kiir release my comrades who are under detention and let them be evacuated to Addis Ababa and we can start dialogue straightaway, because these are the people who would (handle) dialogue." His list of detainees to be released included Pagan Amum and Rebecca Garang, of whom Makeui said: "They are criminals who must be brought to the books, so there is no way we can negotiate with (Machar)." Meanwhile, UNMISS spokesman, Joe Contreras, added: "For those elements who are trying to intimidate us or who have attacked us, the message is loud and clear: we are here to serve the people of South Sudan and we are not leaving the country under any circumstances." Machar told Radio France Internationale that the rebel side was ready for talks that could possibly occur in Ethiopia and that he had also spoken to U.S. Secretary of State John Kerry and Ethiopian Foreign Minister Tedros Adhanom. "We want democratic free and fair elections. We want Salva Kiir to call it a day." He added that: "The SPLM is the ruling party and the SPLA is the national army and I believe these two organisations can end the term of President Kiir. President Kiir has failed to unite the people. He is inciting inter-ethnic fighting. Now he is dividing the country. So it is best he leaves, and I believe the SPLA and SPLM can make him leave."
On 24 December, the government of South Sudan claimed to have recaptured Bor, according to Kiir. Aguer said that the army was 11 kilometres (7 mi) outside Bor and would soon advance on the city, and "the other cities will be retaken within 72 hours." He also said that the reports of mass graves would be investigated. There was also tension at the UN compound in the city as armed fighters had entered it and about 17,000 civilians seeking protection were at the location. The day's fighting started at 14:00 and was intense for two hours. The first part of the city recaptured was where the original fighting started, the Pan-pandia SPLA division headquarters and Malual-chaat village, just outside Bor. The claim of victory came at 19:30. Though most of Gadet's troops had left their position, fighting continued around the airport. On the same day, the rebels had also reported in the town of Malakal There continued to be reports of non-military fighters on the streets of Juba's Munuki neighbourhood armed with machetes and knives. Atrocities continue almost daily with reports of ethnic targeting reminiscent of the Second Sudanese Civil War days.
Many of these reports have come from the hundreds of foreign oil company employees gathered at the airport to leave. Five Ugandan and ten Kenyan citizens were also evacuated from Bor and then Juba before leaving the country. The Kenyan government said that there were 30,000 of its nationals in the country and that 10,000 had applied for emergency documents. Kenya, answering complaints that they were not responding sufficiently quickly, stated that their priority was to evacuate women and children, and that it was getting aid to the country as best as it could.
On 25 December, fighting continued in Malakal, according to Ateny, who added that the "oil fields are safe." Makwei said that though "there is fighting now in Malakal since morning between the government forces and the rebels. It is not true that the rebels have taken over." Only four of the 10 states of South Sudan had reported fighting, including the aforementioned Jonglei, Unity, Upper Nile and Central Equatoria, the location of Juba. The UN also reported that renewed fighting and deteriorating conditions in Jonglei occurred south of Bor and that their base was being reinforced with additional protective barriers, including the area hosting the displaced civilians.
On 27 December, the army said it had taken back full control of Malakal, the administrative center of Upper Nile, a state which currently supplies all of South Sudan's crude oil, after fighting shut down oil fields in other areas. "Government forces are 100 percent in control of Malakal town and are pursuing the forces of the coup," Aguer said by phone in South Sudan capital Juba. On the same day, Machar, in an interview with Sudan Tribune, said a Ugandan MiG-29 bombed their positions around South Sudan Jonglei state capital, Bor, which they temporarily captured before it was retaken by forces loyal to president Salva Kiir. "Our positions around Jonglei state capital, Bor, have been bombed by MiG  jet fighter of the Uganda People's Defence Force (UPDF) at around 2pm", Machar said. "We don't yet know the number of casualties", he added. The ex-deputy president condemned what he described as interference by Ugandan forces into South Sudan's internal affairs.
On 29 December, a U.N. helicopter spotted a group of armed youths 50 kilometres (31 mi) from Bor but could not confirm their numbers. Meanwhile, rebels were mobilising youths and armed civilians for another attack on Malakal, the army said. Rebels had been pushed out of the town on Friday.
On 30 December, South Sudanese government troops clashed with ethnic White Army militiamen and other rebel factions loyal to Machar late on Monday near the flashpoint town of Bor, government officials said. Shootings have taken place just outside, to the north of Bor, Aguer said by phone from Juba, 190 kilometres (120 mi) south of Bor by road. Earlier Aguer told Reuters there was fighting in the town. Information Minister Michael Makuei also said SPLA troops clashed with rebels on the edge of the Jonglei state capital. Bor town Mayor Nhial Majak Nhial said there was no fighting in the town center from where he spoke to Reuters by phone. A rebel spokesman has denied Machar controls the White Army militiamen.
On 31 December, South Sudanese rebels battled their way to the centre of the strategically important town of Bor and were in control of some neighbourhoods as the fighting continued, Mayor Nhial and Information Minister Michael Makuei.
On 2 January 2014, South Sudanese rebels loyal to Machar seized control of Bor, Nhial said on Wednesday, while government troops had made a "tactical withdrawal" to Malual Chaat army barracks, 3 kilometres (1.9 mi) south of the town, after fighting that started earlier in the day. "Yes they (rebels) have taken Bor," Nhial said from Juba. On the same day, Kiir declared a state of emergency in Unity and Jonglei states, where Machar- aligned rebels controlled the capitals. Machar said that his force clashed with the SPLA 25 km (15 miles) outside Bor, destroying a large military convoy.
On 4 January intense battles involving tanks and artillery were reported on the outskirts of Bor, which by this time had changed hands three times since fighting in as many weeks. Rebels claimed that a South Sudanese army general has been killed in the fighting, as his convoy approaching Bor was ambushed. The SPLA brought large numbers of reinforcements bringing the total SPLA troops 25 km (15 miles) Bor close to 2,000.
On 8 January, fighting continued in Upper Nile state while more troops previously based in Juba had defected and could launch an assault on the capital according to rebel spokesman Moses Ruai Lat, who also said that anti-government fighters were preparing to strike at Malakal. Aguer only confirmed that fighting continued to rage around Bor.
On 10 February 2014, the UN base in Juba was surrounded by armed government troops and policemen, who demanded that the UN surrender Nuer civilians sheltering there. On 18 February 2014, fighting between members of various ethnicities broke out within the UN Mission in the capital city of Upper Nile State, Malakal, resulting in ten deaths.
By this time, the UN compound in Malakal housed around 20,000 people who had fled the conflict, according to UN spokesman Martin Nesirky. The UNMISS reported that on 14 January heavy fighting broke out near the UN compound in Malakal. Rebel forces claimed to have recaptured Malakal from the army, while army forces claimed to have held the city after heavy fighting. In the course of this battle, dozens of refugees in the UN compound were injured and a Nile ferry carrying fleeing refugees sank in the river, drowning more than 200 people.
Mayom county has seen the most entrenched clashes in Unity State, with both sides making repeated claims that they are in control of the county. Many of the most important politicians in Unity come from Mayom County, including Nugen Monytuel, the governor of Unity, and much of the SSLM/A. Following the defection of the majority of the SPLA’s 4th division, Monytuel escaped to Mayom county himself.
Mayom county was initially under the control of the rebel forces, while the remaining elements of the 4th division still loyal to Salva Kiir regrouped in Abiemnom county. SPLA-loyalists received a boost when rebel South Sudan Liberation Movement (SSLA) forces, led by the Bul Nuer commander Matthew Puljang, decided to support them.
On 27 December, the combined SSLA/SPLA force clashed with rebels in Mayom, a strategic town and important trading hub some 90 kilometres (56 mi) from Unity State capital Bentiu, leading to extensive destruction, including of the main market. Rebels advanced on 29 December to seize Mayom, but by 6 January the town was almost entirely destroyed, and the front lines had moved east, towards Tumur. Peter Dak -rebel commander in Mayom- announced that he fled the town on the evening of 7 January. On 9 January, SPLA forces attacked rebel positions at Tor al- Abyad, about 30 kilometres (19 mi) to the west of Bentiu.
The advance of the SPLA caused panic in Bentiu. On 8–9 January, thousands of civilians fled the city in expectation of further clashes. The rebels became increasingly disorganized. Armed men looted stalls and shops in Bentiu's market while rebel forces brought a tank into the town to help defend it from the anticipated government attack. Bentiu had been mostly evacuated by 10 January, with even the main hospital being abandoned.
On 8 January, much of the rebel force retreated, destroying ammunition dumps along the way, to stop them falling into the hands of the SPLA. On 10 January, fighting resumed on the outskirts of Bentiu. The SPLA force attacking Bentiu was composed of reinforcements from the 3rd and 5th divisions, and the remnants of the 4th division still loyal to the government. The SPLA entered Bentiu in the afternoon, with the rebel forces, including rebel commander Koang Chuol, in full retreat. By the end of the day on 10 January, the SPLA had secured the city.
On 11 January, part of the SPLA garrison at Doleib Hill defected leading to a firefight within the base, which was also the site of George Athor's initial revolt. Later that same day Lt. General Johnson Gony Biliu, Commander of the SPLA's 7th Division, was ambushed while he was departing Malakal in a large convoy.
On 13 January, South Sudanese troops advanced on Bor, the last state capital still in rebel hands, as ceasefire talks in neighbouring Ethiopia were called off for the day.
On 15 January, fighting continued in the streets of Malakal  with both sides claiming to control the town as the conflict entered its second month. Civilians emptied out of the town, and at least 200 drowned when their overcrowded boat sank as they tried to flee across the Nile. One civilian was killed and dozens of civilians and a security officer were wounded inside the Malakal UNMISS base by gunfire from outside. UNMISS security returned warning shots.
On 16 January, Uganda's president Yoweri Museveni, and UPDF spokesman Lieutenant Colonel Paddy Ankunda said that UPDF troops had joined the SPLA in the fight for Bor. This admission came after frequent December denials of military involvement. Uganda had claimed troops presence was to vacate 2,000 Ugandan civilians trapped in South Sudan. IGAD has demanded the removal of Ugandan troops from South Sudan. IGAD nation Ethiopia is opposed to that Ugandan involvement warning it may incite regional conflict.
On 17 January, South Sudanese troops said it had lost contact with forces in Malakal, which both rebels and the government claim to control.
January 2014 ceasefire agreement
In order to ensure a stronger negotiating position, South Sudanese troops fighting alongside Ugandan troops retook every town held by the rebels, including Bor on January 18 and Malakal on January 20. On 23 January 2014, representatives of the Government of South Sudan and representatives of rebel leader Riek Machar reached a ceasefire agreement in Ethiopia. The deal also stipulated that 11 officials close to rebel leader Machar should be released.
Only a few days later, the rebels accused that a government takeover of Leer was a deliberate attempt to sabotage the second round of talks that were to start later in February. The rebels threatened to boycott the second round talks, demanding the release of four remaining political prisoners and the withdrawal of Ugandan troops. Later in February, the rebels attacked the strategic government controlled Malakal and the government admitted withdrawal and then, in March, the rebels admitted withdrawal, changing hands for the fifth time.
In April, rebels claimed once again to have seized Bentiu and by April 19 South Sudan's army admitted to have "lost communication" with commanders battling in Unity state. The 2014 Bentiu massacre occurred on 15 April in Bentiu when more than 200 civilians were massacred by Neur rebels. A mosque, hospital, and church were targeted where civilians had sought refuge from the fighting. All the victims were said to have been of Dinka ethnicity. After the fall of Bentiu, Salva Kiir sacked Army chief James Hoth Mai and replaced him with Paul Malong Awan.
On 9 May 2014, President Salva Kiir and Riek Machar signed the second ceasefire in Addis Ababa, a one-page agreement recommitting to the first ceasefire. Hostilities were to end in 24 hours while a permanent ceasefire would be worked on and it promised to open humanitarian corridors and allow “30 days of tranquility” so farmers can sow crops and prevent famine. Hours after the ceasefire was to be in effect, both sides accused each other of violating the ceasefire.
On 11 June 2014, both parties agreed to begin talks on the formation of a transitional government within 60 days and to a third ceasefire refraining from combat during this period. However, the talks collapsed as both sides boycotted the talks, and by 16 June, the ceasefire was reported to have been violated.
In August 2014, Kiir and leaders of South Sudan’s neighbouring states sign a roadmap leading to a transitional government of national unity. Machar refuses to sign up, accusing leaders in the Intergovernmental Authority on Development (IGAD), a regional group involved in the negotiations, of tilting the process in favour of Kiir.
In November 2014, both parties renew the much-broken ceasefire and IGAD mediators give them 15 days to reach a power-sharing deal, threatening sanctions if they fail. This third ceasefire breaks down 24 hours later with fighting in the oil-rich north.
In February 2015, Kiir and Machar sign a document in the Ethiopian capital, Addis Ababa, on “Areas of Agreement” for a future transitional government of national unity. They recommit themselves to the ceasefire but fail to agree on sharing power. The talks later collapsed and fighting broke out in March.
Johnson Olony led a militia that planned to be integrated into the SPLM government forces, but he switched to oppose the government, and on 16 May 2015, his militia and elements of the SPLM-IO captured Upper Nile's capital, Malakal, as well as Anakdiar and areas around Kodok. His Shilluk militia group now called itself the 'Agwelek forces'. The group said they want to run their affairs independently from others in Upper Nile State, and SPLM-IO backed away from claims that it is in charge of Olony's group and stated that Olony's interests simply coincides with theirs. SPLM-IO said they understood the feeling from the Shilluk community that they wanted a level of independence and that that was the reason the SPLM-IO last year created Fashoda state for the Shilluk kingdom and appointed Tijwog Aguet, a Shilluk, as governor.
On 11 August 2015, Gathoth Gatkuoth, the former SPLM-IO logistics chief, and rebel commander Peter Gadet, announced that they and other powerful commanders had split from Riek Machar, believing him to be "seeking power for himself". They rejected ongoing peace talks and announced that they would now combat Riek Machar's forces in addition to government forces, saying, "They (Riek Machar and President Salva Kiir) are symbols of hate, division and failed leadership, both leaders were responsible for starting the crisis." Gathoth Gatkuoth states he wishes for a President who is neither Dinka nor Nuer. Gatkuoth states that he intends to register his group as a political group called the "Federal Democractic Party" and that their forces would be called the "South Sudan National Army".
August 2015 peace agreement
In late August 2015, Salvar Kiir signed a peace agreement previously signed by Riek Machar called the "Compromise Peace Agreement" mediated by "IGAD +" (which includes the eight regional nations as well as the United Nations, the African Union, China, the EU, USA, UK and Norway). The agreement would make Riek Machar the vice-president again.
Massacres of civilians
The Guardian and BBC reported that 240 Nuer men were rounded up and killed at a police station in Juba in mid-December 2013. UN Assistant General Secretary Ian Simonovic has cited and confirmed these survivor stories in an opinion article into the Gudele massacre. Official death toll has not been released as South Sudan government troops have blocked access to Gudele and other affected, now abandoned suburbs of Juba. The Guardian report also reported that 21 Nuer youths as well as three women were killed in two other incidents. This number sets to grow, as Human Rights Watch article cites eye witness accounts of truck loads of bodies carried to undisclosed site on December 18, 2013, shortly after the Gudele massacre of Nuer civilians. The location of the burial cites is unknown. Numbers of the dead in Juba now exceed initial estimates. Human Rights Watch has noted the South Sudan government has sealed off access to Nuer suburbs where the genocide began. The affected neighborhoods are heavily guarded with armed security presence, hampering reporting and independent investigation. Government officials have not announced a list of the dead or the location of the bodies. Claiming ignorance of killings, Phillip Aguer, the SPLA spokesman, denied any organized attacks had taken place. He said he was unaware of the slaughter at Mangaten police station and blamed any deaths on "criminal elements" who had exploited the instability as an opportunity loot and kill. His comments come in direct opposition to UN Assistant General Secretary, Ian Simonovic report. Claims by Aguer also are at odds with survivor accounts, and Human Rights Watch Reports. Armed government soldiers have been noted roaming the suburbs in an "undisciplined and threatening manner."
Ateny Wek Ateny, president's spokesman told to news conference, claims that rebel troops went into the hospital in the town of Bor last month and slaughtered 126 out of 127 patients. Apparently an elderly man was blind and rebels spared him. January 31, 2014 in violation cease fire agreement,the signed Government troops attacked town of Leer in Unity State, forcing 240 Staff and patients of Doctors Without Borders in Leer to flee into the bush. Thousands of civilians have flet to the bush. Doctors Without Borders has lost contact with two thirds of its staff formerly located in Leer. It is believed that the town was attacked by government troops as it is the home of former Vice President Riek Machar. On 18 April, UN said that at least 58 people were killed and more than 100 others wounded in an attack against one of its bases in South Sudan sheltering thousands of civilians.
200 people were killed in a mosque when Bentiu was recaptured by rebels on 16 April and an unspecified number were also killed at a hospital. Rebels separated the people and picked out those from opposing ethnic groups who they then executed.
On 17 April 2014, 58 people were killed in an attack on the UN base in Bor. 48 of those killed were civilians, while 10 were among the attackers. UN Secretary-General Ban Ki-moon emphasised that any attack on UN peacekeepers constituted "a war crime", while the UN Security Council expressed "outrage" at the attack.
On 26 August 2014, a UN Mi-8 cargo helicopter was shot down, killing 3 Russian crew members, and wounding another. This occurred 9 days after rebel commander Peter Gadet threatened to shoot down UN aircraft, which he alleged were transporting government forces.
During the first two days of fighting, reports indicated that 66 soldiers had been killed in clashes in Juba, but that number was complemented by between 400 and 500 people, mostly soldiers, according to a government official and UN diplomats quoting sources in Juba, and at least 800 injured. Two Indian UN peacekeepers were killed on 18 December when their base was stormed by rebels, and three US military Osprey aircraft were fired upon leading to four American service personnel being wounded.
On 23 December, the UN's humanitarian coordinator stated the number of dead had likely surpassed 1,000 people while an aid worker in the country estimated that the death toll was most likely in the tens of thousands. On 24 December, the UN's Navi Pillay claimed that the bodies of 75 government soldiers were discovered in a mass grave in Bentiu, while another two mass graves were reportedly found in Juba. The United Nations High Commissioner for Refugees's Ravina Shamdasani said an unnamed official had seen over 30 bodies in the two mass graves and its existence was being verified. "It is very difficult, and there are reports that some bodies may have already been burned." On 25 December, UNMISS denied the report of a mass grave that was issued by UNHCR. At the same time, Pillay's office revised down the figure of dead bodies to 34 bodies and 75 people were feared missing.
On 26 December, Hilde Frafjord Johnson, head of the United Nations Mission in South Sudan, also confirmed estimates that well over 1,000 people had died in 12 days of fighting, while dismissing reports that the death toll was in the multiple thousands.
The International Crisis Group reported on 9 January that up to 10,000 people were estimated to have died.
In addition to those wounded or killed, the United Nations Office for the Coordination of Humanitarian Affairs has stated that about 413,000 people are internally displaced, 66,500 are seeking refuge at United Nations bases around the country, and more than 74,300 have fled the country.
In November 2014, the International Crisis Group estimated the death toll could be between 50,000 and 100,000.
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