Politics of independence

Sudan achieved independence without the rival political parties having agreed on the form and content of a permanent constitution. Instead, the Constituent Assembly adopted a document known as the Transitional Constitution, which replaced the governor general as head of state with a five-member Supreme Commission that was elected by a parliament composed of an indirectly elected Senate and a popularly elected House of Representatives. The Transitional Constitution also allocated executive power to the prime minister, who was nominated by the House of Representatives and confirmed in office by the Supreme Commission.

Although it achieved independence without conflict, Sudan inherited many problems from the condominium. Chief among these was the status of the civil service. The government placed Sudanese in the administration and provided compensation and pensions for British officers of the Sudan Political Service who left the country; it retained those who could not be replaced, mostly technicians and teachers. Khartoum achieved this transformation quickly and with a minimum of turbulence, although southerners resented the replacement of British administrators in the south with northern Sudanese. To advance their interests, many southern leaders concentrated their efforts in Khartoum, where they hoped to win constitutional concessions. Although determined to resist what they perceived to be Arab imperialism, they were opposed to violence. Most southern representatives supported provincial autonomy and warned that failure to win legal concessions would drive the south to rebellion.

The parliamentary regime introduced plans to expand the country's education, economic, and transportation sectors. To achieve these goals, Khartoum needed foreign economic and technical assistance, to which the United States made an early commitment. Conversations between the two governments had begun in mid-1957, and the parliament ratified a United States aid agreement in July 1958. Washington hoped this agreement would reduce Sudan's excessive reliance on a one-crop (cotton) economy and would facilitate the development of the country's transportation and communications infrastructure.

The prime minister formed a coalition government in February 1956, but he alienated the Khatmiyyah by supporting increasingly secular government policies. In June some Khatmiyyah members who had defected from the NUP established the People's Democratic Party (PDP) under Mirghani's leadership. The Umma and the PDP combined in parliament to bring down the Azhari government. With support from the two parties and backing from the Ansar and the Khatmiyyah, Abdallah Khalil put together a coalition government.

Major issues confronting Khalil's coalition government included winning agreement on a permanent constitution, stabilizing the south, encouraging economic development, and improving relations with Egypt. Strains within the Umma-PDP coalition hampered the government's ability to make progress on these matters. The Umma, for example, wanted the proposed constitution to institute a presidential form of government on the assumption that Abd ar Rahman al Mahdi would be elected the first president. Consensus was lacking about the country's economic future. A poor cotton harvest followed the 1957 bumper cotton crop, which Sudan had been unable to sell at a good price in a glutted market. This downturn depleted Sudan's reserves and caused unrest over government-imposed economic restrictions. To overcome these problems and finance future development projects, the Umma called for greater reliance on foreign aid. The PDP, however, objected to this strategy because it promoted unacceptable foreign influence in Sudan. The PDP's philosophy reflected the Arab nationalism espoused by Gamal Abdul Nasser, who had replaced Egyptian leader Naguib in 1954. Despite these policy differences, the Umma-PDP coalition lasted for the remaining year of the parliament's tenure. Moreover, after the parliament adjourned, the two parties promised to maintain a common front for the 1958 elections.

a common front for the 1958 elections.

The electorate gave a plurality in both houses to the Umma and an overall majority to the Umma-PDP coalition. The NUP, however, won nearly one-quarter of the seats, largely from urban centers and from Gezira Scheme agricultural workers. In the south, the vote represented a rejection of the men who had cooperated with the government—voters defeated all three southerners in the preelection cabinet—and a victory for advocates of autonomy within a federal system. Resentment against the government's taking over mission schools and against the measures used in suppressing the 1955 mutiny contributed to the election of several candidates who had been implicated in the rebellion.

After the new parliament convened, Khalil again formed an Umma-PDP coalition government. Unfortunately, factionalism, corruption, and vote fraud dominated parliamentary deliberations at a time when the country needed decisive action with regard to the proposed constitution and the future of the south. As a result, the Umma-PDP coalition failed to exercise effective leadership.

Another issue that divided the parliament concerned Sudanese-United States relations. In March 1958, Khalil signed a technical assistance agreement with the United States. When he presented the pact to parliament for ratification, he discovered that the NUP wanted to use the issue to defeat the Umma-PDP coalition and that many PDP delegates opposed the agreement. Nevertheless, the Umma, with the support of some PDP and southern delegates, managed to obtain approval of the agreement.

Factionalism and bribery in parliament, coupled with the government's inability to resolve Sudan's many social, political, and economic problems, increased popular disillusion with democratic government. Specific complaints included Khartoum's decision to sell cotton at a price above world market prices. This policy resulted in low sales of cotton, the commodity from which Sudan derived most of its income. Restrictions on imports imposed to take pressure off depleted foreign exchange reserves caused consternation among town dwellers who had become accustomed to buying foreign goods. Moreover, rural northerners also suffered from an embargo that Egypt placed on imports of cattle, camels, and dates from Sudan. Growing popular discontent caused many antigovernment demonstrations in Khartoum. Egypt also criticized Khalil and suggested that it might support a coup against his government. Meanwhile, reports circulated in Khartoum that the Umma and the NUP were near agreement on a new coalition that would exclude the PDP and Khalil.

On November 17, 1958, the day parliament was to convene, a military coup occurred. Khalil, himself a retired army general, planned the preemptive coup in conjunction with leading Umma members and the army's two senior generals, Ibrahim Abboud and Ahmad Abd al Wahab, who became leaders of the military regime. Abbud immediately pledged to resolve all disputes with Egypt, including the long-standing problem of the status of the Nile River. Abbud abandoned the previous government's unrealistic policies regarding the sale of cotton. He also appointed a constitutional commission, headed by the chief justice, to draft a permanent constitution. Abbud maintained, however, that political parties only served as vehicles for personal ambitions and that they would not be reestablished when civilian rule was restored.

Abbud military government (1958–1964)

The coup removed political decision making from the control of the civilian politicians. Abbud created the Supreme Council of the Armed Forces to rule Sudan. This body contained officers affiliated with the Ansar and the Khatmiyyah. Abbud belonged to the Khatmiyyah, whereas Abd al Wahab was a member of the Ansar. Until Abd al Wahab's removal in March 1959, the Ansar were the stronger of the two groups in the government.

The regime benefited during its first year in office from successful marketing of the cotton crop. Abbud also profited from the settlement of the Nile waters dispute with Egypt and the improvement of relations between the two countries. Under the military regime, the influence of the Ansar and the Khatmiyyah lessened. The strongest religious leader, Abd ar Rahman al Mahdi, died in early 1959. His son and successor, the elder Sadiq al Mahdi, failed to enjoy the respect accorded his father. When Sadiq died two years later, Ansar religious and political leadership divided between his brother, Imam Al Hadi al Mahdi, and his son, the younger Sadiq al Mahdi.

Despite the Abbud regime's early successes, opposition elements remained powerful. In 1959 dissident military officers made three attempts to displace the Abbud government and to establish a "popular government." Although the courts sentenced the leaders of these attempted coups to life imprisonment, discontent in the military continued to hamper the government's performance. In particular, the Sudanese Communist Party (SCP), which supported the attempted coups, gained a reputation as an effective antigovernment organization. To compound its problems, the Abbud regime lacked dynamism and the ability to stabilize the country. Its failure to place capable civilian advisers in positions of authority, to launch a credible economic and social development program, and to gain the army's support created an atmosphere that encouraged political turbulence.

Abbud's southern policy proved to be his undoing. The government suppressed expressions of religious and cultural differences and bolstered attempts to arabize society. In February 1964, for example, Abbud ordered the mass expulsion of foreign missionaries from the south. He then closed parliament to cut off outlets for southern complaints. Southern leaders had renewed in 1963 the armed struggle against the Sudanese government that had continued sporadically since 1955. The rebellion was spearheaded from 1963 by guerrilla forces known as the Anyanya (the name of a poisonous concoction).

Return to civilian rule (1964–1969)

Recognizing its inability to quell growing southern discontent, the Abbud regime asked the civilian sector to submit proposals for a solution to the southern problem. However, criticism of government policy quickly went beyond the southern issue and included Abbud's handling of other problems, such as the economy and education. Government attempts to silence these protests, which were centered in the University of Khartoum, brought a reaction not only from teachers and students but also from Khartoum's civil servants and trade unionists. The so-called October Revolution of 1964 centered around a general strike that spread throughout the country. Strike leaders identified themselves as the National Front for Professionals. Along with some former politicians, they formed the leftist United National Front (UNF), which made contact with dissident army officers.

After several days of rioting that resulted in many deaths, Abbud dissolved the government and the Supreme Council of the Armed Forces. UNF leaders and army commanders who planned the transition from military to civilian rule selected a nonpolitical senior civil servant, Sirr Al-Khatim Al-Khalifa, as prime minister to head a transitional government.

The new civilian regime, which operated under the 1956 Transitional Constitution, tried to end political factionalism by establishing a coalition government. There was continued popular hostility to the reappearance of political parties, however, because of their divisiveness during the Abbud regime. Although the new government allowed all parties, including the SCP, to operate, only five of fifteen posts in Khatim's cabinet went to party politicians. The prime minister gave two positions to nonparty southerners and the remaining eight to members of the National Front for Professionals, which included several communists.

Eventually two political parties emerged to represent the south. The Sudan African National Union (SANU), founded in 1963 and led by William Deng and Saturino Lahure, a Roman Catholic priest, operated among refugee groups and guerrilla forces. The Southern Front, a mass organization led by Stanislaus Payasama that had worked underground during the Abbud regime, functioned openly within the southern provinces. After the collapse of government-sponsored peace conferences in 1965, Deng's wing of SANU—known locally as SANU-William—and the Southern Front coalesced to take part in the parliamentary elections. SANU remained active in parliament for the next four years as a voice for southern regional autonomy within a unified state. Exiled SANU leaders balked at Deng's moderate approach and formed the Azania Liberation Front based in Kampala, Uganda.

Anyanya leaders remained aloof from political movements. The guerrillas were fragmented by ethnic and religious differences. Additionally, conflicts surfaced within Anyanya between older leaders who had been in the bush since 1955, and younger, better educated men like Joseph Lagu, a former Sudanese army captain, who eventually became a strong guerrilla leader, largely because of his ability to get arms from Israel.

The government scheduled national elections for March 1965 and announced that the new parliament's task would be to prepare a new constitution. The deteriorating southern security situation prevented elections from being conducted in that region, however, and the political parties split on the question of whether elections should be held in the north as scheduled or postponed until the whole country could vote. The PDP and SCP, both fearful of losing votes, wanted to postpone the elections, as did southern elements loyal to Khartoum. Their opposition forced the government to resign. The president of the reinstated Supreme Commission, who had replaced Abbud as chief of state, directed that the elections be held wherever possible. The PDP rejected this decision and boycotted the elections.

The 1965 election results were inconclusive. Apart from a low voter turnout, there was a confusing overabundance of candidates on the ballots. As a result, few of those elected won a majority of the votes cast. The Umma captured 75 out of 158 parliamentary seats while its NUP ally took 52 of the remainder. The two parties formed a coalition cabinet in June headed by Umma leader Muhammad Ahmad Mahjub, whereas Azhari, the NUP leader, became the Supreme Commission's permanent president and chief of state.

The Mahjub government had two goals: progress toward solving the southern problem and the removal of communists from positions of power. The army launched a major offensive to crush the rebellion and in the process augmented its reputation for brutality among the southerners. Many southerners reported government atrocities against civilians, especially at Juba and Wau. Sudanese army troops also burned churches and huts, closed schools, and destroyed crops and cattle. To achieve his second objective, Mahjub succeeded in having parliament approve a decree that abolished the SCP and deprived the eleven communists of their seats.

In October 1965, the Umma-NUP coalition collapsed because of a disagreement over whether Mahjub, as prime minister, or Azhari, as president, should conduct Sudan's foreign relations. Mahjub continued in office for another eight months but resigned in July 1966 after a parliamentary vote of censure, which resulted in a split in the Umma. The traditional wing led by Mahjub, under the Imam Al Hadi al Mahjub's spiritual leadership, opposed the party's majority. The latter group professed loyalty to the Imam's nephew, the younger Sadiq al Mahdi, who was the Umma's official leader and who rejected religious sectarianism. Sadiq became prime minister with backing from his own Umma wing and from NUP allies.

The Sadiq al Mahdi government, supported by a sizable parliamentary majority, sought to reduce regional disparities by organizing economic development. Sadiq al Mahdi also planned to use his personal rapport with southern leaders to engineer a peace agreement with the insurgents. He proposed to replace the Supreme Commission with a president and a southern vice president and called for the approval of autonomy for the southern provinces.

The educated elite and segments of the army opposed Sadiq al Mahdi because of his gradualist approach to Sudan's political, economic, and social problems. Leftist student organizations and the trade unions demanded the creation of a socialist state. Although these elements lacked widespread popular support, they represented an influential portion of educated public opinion. Their resentment of Sadiq increased when he refused to honor a Supreme Court ruling that overturned legislation banning the SCP and ousting communists elected to parliamentary seats. In December 1966, a coup attempt by communists and a small army unit against the government failed. The government subsequently arrested many communists and army personnel.

In March 1967, the government held elections in thirty-six constituencies in pacified southern areas. The Sadiq al Mahdi wing of the Umma won fifteen seats, the federalist SANU ten, and the NUP five. Despite this apparent boost in his support, however, Sadiq's position in parliament had become tenuous because of concessions he promised to the south in order to bring an end to the civil war. The Umma traditionalist wing opposed Sadiq al Mahdi because of his support for constitutional guarantees of religious freedom and his refusal to declare Sudan an Islamic state. When the traditionalists and the NUP withdrew their support, his government fell. In May 1967, Mahjub became prime minister and head of a coalition government whose cabinet included members of his wing of the Umma, of the NUP, and of the PDP. In December 1967, the PDP and the NUP formed the Democratic Unionist Party (DUP) under Azhari's leadership.

By early 1968, widening divisions in the Umma threatened the survival of the Mahjub government. Sadiq al Mahdi's wing held a majority in parliament and could thwart any government action. Mahjub therefore dissolved parliament. However, Sadiq refused to recognize the legitimacy of the prime minister's action. As a result, two governments functioned in Khartoum—one meeting in the parliament building and the other on its lawn—both of which claimed to represent the legislature's will. The army commander requested clarification from the Supreme Court regarding which of them had authority to issue orders. The court backed Mahjub's dissolution; the government scheduled new elections for April.

Although the DUP won 101 of 218 seats, no single party controlled a parliamentary majority. Thirty-six seats went to the Umma traditionalists, thirty to the Sadiq wing, and twenty-five to the two southern parties—SANU and the Southern Front. The SCP secretary general, Abd al Khaliq Mahjub, also won a seat. In a major setback, Sadiq lost his own seat to a traditionalist rival.

Because it lacked a majority, the DUP concluded an alliance with Umma traditionalists, who received the prime ministership for their leader, Muhammad Ahmad Mahjub, and four other cabinet posts. The coalition's program included plans for government reorganization, closer ties with the Arab world, and renewed economic development efforts, particularly in the southern provinces. The Muhammad Ahmad Mahjub government also accepted military, technical, and economic aid from the Soviet Union. Sadiq al Mahdi's wing of the Umma formed the small parliamentary opposition. When it refused to participate in efforts to complete the draft constitution, already ten years overdue, the government retaliated by closing the opposition's newspaper and clamping down on pro-Sadiq demonstrations in Khartoum.

By late 1968, the two Umma wings agreed to support the Ansar chief Imam Al Hadi al Mahdi in the 1969 presidential election. At the same time, the DUP announced that Azhari also would seek the presidency. The communists and other leftists aligned themselves behind the presidential candidacy of former Chief Justice Babiker Awadallah, whom they viewed as an ally because he had ruled against the government when it attempted to outlaw the SCP.

The First Sudanese Civil War

The First Sudanese Civil War (also known as the Anyanya Rebellion or Anyanya I, after the name of the rebels) was a conflict from 1955 to 1972 between the northern part of Sudan and the southern Sudan region that demanded representation and more regional autonomy. Half a million people died over the 17 years of war, which may be divided into three stages: initial guerrilla war, Anyanya, and South Sudan Liberation Movement.

However, the agreement that ended the First Sudanese Civil War's fighting in 1972 failed to completely dispel the tensions that had originally caused it, leading to a reigniting of the north-south conflict during the Second Sudanese Civil War, which lasted from 1983 to 2005. The period between 1955 and 2005 is thus sometimes considered to be a single conflict with an eleven-year ceasefire that separates two violent phases.

Origins of the conflict

Until 1946, the British government, in collaboration with the Egyptian government (under a condominium governing arrangement) administered south Sudan and north Sudan as separate regions. At this time, the two areas were merged into a single administrative region as part of British strategy in the Middle East.

This act was taken without consultation with southerners, who feared being subsumed by the political power of the larger north. Southern Sudan is inhabited primarily by Christians and animists and considers itself culturally sub-Saharan, while most of the north is inhabited by Muslims who were culturally Arabic.

After the February 1953 agreement by the United Kingdom and Egypt to grant independence to Sudan, the internal tensions over the nature of the relationship of north to south were heightened. Matters reached a head as the 1 January 1956 independence day approached, as it appeared that northern leaders were backing away from commitments to create a federal government that would give the south substantial autonomy.

Course of the war

On 18 August 1955, members of the British-administered Sudan Defence Force Equatorial Corps mutinied in Torit, and in the following days in Juba, Yei, and Maridi. The immediate causes of the mutiny were a trial of a southern member of the national assembly and an allegedly false telegram urging northern administrators in the South to oppress Southerners.The mutinies were suppressed, though survivors fled the towns and began an uncoordinated insurgency in rural areas. Poorly armed and ill-organized, they were little threat to the outgoing colonial power or the newly formed Sudanese government. O'Ballance, writing in 1977, says that the 'period from 1955 to 1963 was simply one of guerilla survival, scarcely removed from banditry, and that it was successful due to a score or so of former southern army officers and warrant officers, and a small number of non-commissioned officers.

However, the insurgents gradually developed into a secessionist movement composed of the 1955 mutineers and southern students. These groups formed the Anyanya guerrilla army. (Anyanya is also known as Anyanya 1 in comparison to Anyanya 2, began with the 1974 mutiny of the military garrison in Akobo.) Starting from Equatoria, between 1963 and 1969 Anyanya spread throughout the other two southern provinces: Upper Nile and Bahr al Ghazal. However, the separatist movement was crippled by internal ethnic divisions. O'Ballance writes that one of the Sudanese army's four infantry brigades had been stationed in Equatoria Province since 1955, being periodically reinforced as required.

The government was unable to take advantage of rebel weaknesses because of their own factionalism and instability. The first independent government of Sudan, led by Prime Minister Ismail al-Azhari, was quickly replaced by a stalemated coalition of various conservative forces, which was in turn overthrown in the coup d'état of Chief of Staff Lt. Gen. Ibrahim Abboud in 1958. Resentment at the military government led to a wave of popular protests that led to the creation of an interim government in October 1964.

These protests were the first appearance of Islamist Hassan al-Turabi, who was then a student leader. Between 1966 and 1969, a series of Islamist-dominated administrations proved unable to deal with the variety of ethnic, economic and conflict problems afflicting the country. After a second military coup on 25 May 1969, Col. Gaafar Nimeiry became Prime Minister and promptly outlawed political parties.[citation needed]

In-fighting between Marxist and non-Marxist factions in the ruling military class led to another coup in July 1971 and a short-lived administration by the Sudanese Communist Party before anti-Communist factions put Nimeiry back in control of the country. That same year, German national Rolf Steiner, who had been clandestinely advising the rebels, was captured in Kampala, Uganda and deported to Khartoum, where he was put on trial for his anti-government activities. Originally sentenced to death, he would serve three years in prison before being released following pressure from the West German Government.

In 1971, former army lieutenant Joseph Lagu gathered all the guerilla bands under his Southern Sudan Liberation Movement (SSLM). This was the first time in the history of the war that the separatist movement had a unified command structure to fulfill the objectives of secession and the formation of an independent state in South Sudan. It was also the first organization that could claim to speak for, and negotiate on behalf of, the entire south. Mediation between the World Council of Churches (WCC) and the All Africa Conference of Churches (AACC), both of which spent years building up trust with the two combatants, eventually led to the Addis Ababa Agreement of March 1972 ending the conflict. In exchange for ending their armed uprising, southerners were granted a single southern administrative region with various defined powers.

Effects of the war

Five hundred thousand people, of which only one in five was considered an armed combatant, were killed in the seventeen years of war and hundreds of thousands more were forced to leave their homes. The Addis Ababa Agreement proved to be only temporary respite. Infringements by the north led to increased unrest in the south starting in the mid-1970s, leading to the 1983 army mutiny that sparked the Second Sudanese Civil War.

Politics of Sudan (1969–1985)

 Nimeiri era

On May 25, 1969, several young officers calling themselves the Free Officers Movement seized power in Sudan and started the Nimeiri era in the history of Sudan. At the conspiracy's core were nine officers led by Colonel Jaafar an Nimeiri, who had been implicated in plots against the Abboud regime. Nimeiri's coup preempted plots by other groups, most of which involved army factions supported by the Sudanese Communist Party (SCP), Arab nationalists, or conservative religious groups. He justified the coup on the grounds that civilian politicians had paralyzed the decision-making process, had failed to deal with the country's economic and regional problems, and had left Sudan without a permanent constitution.

Revolutionary Command Council

The coup leaders, joined by Babiker Awadallah, the former chief justice who had been privy to the coup, constituted themselves as the ten-member Revolutionary Command Council (RCC), which possessed collective executive authority under Nimeiri's chairmanship. On assuming control, the RCC proclaimed the establishment of a "democratic republic" dedicated to advancing independent "Sudanese socialism." The RCC's first acts included the suspension of the Transitional Constitution, the abolition of all government institutions, and the banning of political parties. The RCC also nationalized many industries, businesses, and banks. Furthermore, Nimeiri ordered the arrest of sixty-three civilian politicians and forcibly retired senior army officers.

Awadallah, appointed prime minister to form a new government to implement RCC policy directives, wanted to dispel the notion that the coup had installed a military dictatorship. He presided over a twenty-one-member cabinet that included only three officers from the RCC, among them its chairman, Nimeiri, who was also defense minister. The cabinet's other military members held the portfolios for internal security and communications. Nine members of the Awadallah regime were allegedly communists, including one of the two southerners in the cabinet, John Garang, minister of supply and later minister for southern affairs. Others identified themselves as Marxists. Since the RCC lacked political and administrative experience, the communists played a significant role in shaping government policies and programs. Despite the influence of individual SCP members, the RCC claimed that its cooperation with the party was a matter of convenience.

In November 1969, after he claimed the regime could not survive without communist assistance, Awadallah lost the prime ministership. Nimeiri, who became head of a largely civilian government in addition to being chief of state, succeeded him. Awadallah retained his position as RCC deputy chairman and remained in the government as foreign minister and as an important link with leftist elements.

Conservative forces, led by the Ansar, posed the greatest threat to the RCC. Imam Al Hadi al Mahdi had withdrawn to his Aba Island stronghold in the Nile, near Khartoum, in the belief that the government had decided to strike at the Ansar movement. The Imam had demanded a return to democratic government, the exclusion of communists from power, and an end to RCC rule. In March 1970, hostile Ansar crowds prevented Nimeiri from visiting the island for talks with the imam. Fighting subsequently erupted between government forces and as many as 30,000 Ansar. When the Ansar ignored an ultimatum to surrender, army units with air support assaulted Aba Island. About 3,000 people died during the battle. The Imam escaped only to be killed while attempting to cross the border into Ethiopia. The government exiled Sadiq al Mahdi to Egypt, where Nasser promised to keep him under guard to prevent him from succeeding his uncle as head of the Ansar movement.

After neutralizing this conservative opposition, the RCC concentrated on consolidating its political organization to phase out communist participation in the government. This strategy prompted an internal debate within the SCP. The orthodox wing, led by party secretary general Abd al Khaliq Mahjub, demanded a popular front government with communists participating as equal partners. The National Communist wing, on the other hand, supported cooperation with the government.

Soon after the army had crushed the Ansar at Aba Island, Nimeiri moved against the SCP. He ordered the deportation of Abd al Khaliq Mahjub. Then, when the SCP secretary general returned to Sudan illegally after several months abroad, Nimeiri placed him under house arrest. In March 1971, Nimeiri indicated that trade unions, a traditional communist stronghold, would be placed under government control. The RCC also banned communist affiliated student, women's, and professional organizations. Additionally, Nimeiri announced the planned formation of a national political movement called the Sudan Socialist Union (SSU), which would assume control of all political parties, including the SCP. After this speech, the government arrested the SCP's central committee and other leading communists.

The SCP, however, retained a covert organization that was not damaged in the sweep. Before further action could be taken against the party, the SCP launched a coup against Nimeiri. The coup occurred on July 19, 1971, when one of the plotters, Major Hisham al Atta, surprised Nimeiri and the RCC meeting in the presidential palace and seized them along with a number of pro-Nimeiri officers. Atta named a seven-member revolutionary council, in which communists ranked prominently, to serve as the national government. Three days after the coup, however, loyal army units stormed the palace, rescued Nimeiri, and arrested Atta and his confederates. Nimeiri, who blamed the SCP for the coup, ordered the arrest of hundreds of communists and dissident military officers. The government subsequently executed some of these individuals and imprisoned many others.

Having survived the SCP-inspired coup, Nimeiri reaffirmed his commitment to establishing a socialist state. A provisional constitution, published in August 1971, described Sudan as a "socialist democracy" and provided for a presidential form of government to replace the RCC. A plebiscite the following month elected Nimeiri to a six-year term as president.

The Southern Problem

The origins of the civil war in the south date back to the 1950s. On August 18, 1955, the Equatoria Corps, a military unit composed of southerners, mutinied at Torit. Rather than surrender to Sudanese government authorities, many mutineers disappeared into hiding with their weapons, marking the beginning of the first war in southern Sudan. By the late 1960s, the war had resulted in the deaths of about 500,000 people. Several hundred thousand more southerners hid in the forests or escaped to refugee camps in neighboring countries.

By 1969 the rebels had developed foreign contacts to obtain weapons and supplies. Israel, for example, trained Anyanya recruits and shipped weapons via Ethiopia and Uganda to the rebels. The Anyanya also purchased arms from Congolese rebels and international arms dealers with monies collected in the south and from among southern Sudanese exile communities in the Middle East, Western Europe, and North America. The rebels also captured arms, equipment, and supplies from government troops.

Militarily, the Anyanya controlled much of the southern countryside while government forces occupied the region's major towns. The guerrillas operated at will from remote camps. However, rebel units were too small and scattered to be highly effective in any single area. Estimates of Anyanya personnel strength ranged from 5,000 to 10,000.

Government operations against the rebels declined after the 1969 coup. However, when negotiations failed to result in a settlement, Khartoum increased troop strength in the south to about 12,000 in 1969, and intensified military activity throughout the region. Although the Soviet Union had concluded a US$100 million to US$150 million arms agreement with Sudan in August 1968, which included T-55 tanks, armored personnel carriers, and aircraft, the nation failed to deliver any equipment to Khartoum by May 1969. During this period, Sudan obtained some Soviet-manufactured weapons from Egypt, most of which went to the Sudanese air force. By the end of 1969, however, the Soviet Union had shipped unknown quantities of 85mm antiaircraft guns, sixteen MiG-21s, and five Antonov-24 transport aircraft. Over the next two years, the Soviet Union delivered an impressive array of equipment to Sudan, including T-54, T-55, T-56, and T-59 tanks; and BTR-40 and BTR-152 light armored vehicles.

In 1971 Joseph Lagu, who had become the leader of southern forces opposed to Khartoum, proclaimed the creation of the Southern Sudan Liberation Movement (SSLM). Anyanya leaders united behind him, and nearly all exiled southern politicians supported the SSLM. Although the SSLM created a governing infrastructure throughout many areas of southern Sudan, real power remained with Anyanya, with Lagu at its head.

Despite his political problems, Nimeiri remained committed to ending the southern insurgency. He believed he could stop the fighting and stabilize the region by granting regional self-government and undertaking economic development in the south. By October 1971, Khartoum had established contact with the SSLM. After considerable consultation, a conference between SSLM and Sudanese government delegations convened at Addis Ababa, Ethiopia, in February 1972. Initially, the two sides were far apart, the southerners demanding a federal state with a separate southern government and an army that would come under the federal president's command only in response to an external threat to Sudan. Eventually, however, the two sides, with the help of Ethiopia's Emperor Haile Selassie, reached an agreement.

The Addis Ababa accords guaranteed autonomy for a southern region--composed of the three provinces of Equatoria (present-day Al Istiwai), Bahr al Ghazal, and Upper Nile (present-day Aali an Nil)--under a regional president appointed by the national president on the recommendation of an elected Southern Regional Assembly. The High Executive Council or cabinet named by the regional president would be responsible for all aspects of government in the region except such areas as defense, foreign affairs, currency and finance, economic and social planning, and interregional concerns, authority over which would be retained by the national government in which southerners would be represented. Southerners, including qualified Anyanya veterans, would be incorporated into a 12,000-man southern command of the Sudanese army under equal numbers of northern and southern officers. The accords also recognized Arabic as Sudan's official language, and English as the south's principal language, which would be used in administration and would be taught in the schools.

Although many SSLM leaders opposed the settlement, Lagu approved its terms and both sides agreed to a cease-fire. The national government issued a decree legalizing the agreement and creating an international armistice commission to ensure the well-being of returning southern refugees. Khartoum also announced an amnesty, retroactive to 1955. The two sides signed the Addis Ababa Agreement on March 27, 1972, which was thereafter celebrated as National Unity Day.

Political Developments

After the settlement in the south, Nimeiri attempted to mend fences with northern Muslim religious groups. The government undertook administrative decentralization, popular with the Ansar, that favored rural over urban areas, where leftist activism was most evident. Khartoum also reaffirmed Islam's special position in the country, recognized the sharia as the source of all legislation, and released some members of religious orders who had been incarcerated. However, a reconciliation with conservative groups, which had organized outside Sudan under Sadiq al Mahdi's leadership and were later known as the National Front, eluded Nimeiri.

In August 1972, Nimeiri sought to consolidate his position by creating a Constituent Assembly to draft a permanent constitution. He then asked for the government's resignation to allow him to appoint a cabinet whose members were drawn from the Constituent Assembly. Nimeiri excluded individuals who had opposed the southern settlement or who had been identified with the SSU's pro-Egyptian faction.

In May 1973, the Constituent Assembly promulgated a draft constitution. This document provided for a continuation of presidential government, recognized the SSU as the only authorized political organization, and supported regional autonomy for the south. The constitution also stipulated that voters were to choose members for the 250-seat People's Assembly from an SSU-approved slate. Although it cited Islam as Sudan's official religion, the constitution acknowledged Christianity as the faith of a large number of Sudanese citizens. In May 1974, voters selected 125 members for the assembly; SSU-affiliated occupational and professional groups named 100; and the president appointed the remaining 25.

Discontent with Nimeiri's policies and the increased military role in government escalated as a result of food shortages and the southern settlement, which many Muslim conservatives regarded as surrender. In 1973 and 1974 there were unsuccessful coup attempts against Nimeiri. Muslims and leftist students also staged strikes against the government. In September 1974, Nimeiri responded to this unrest by declaring a state of emergency, purging the SSU, and arresting large numbers of dissidents. Nimeiri also replaced some cabinet members with military personnel loyal to him.

Conservative opposition to Nimeiri coalesced in the National Front, formed in 1974. The National Front included people from Sadiq's wing of Umma; the National Unionist Party; and the Islamic Charter Front, at the time the political arm of the Muslim Brotherhood. Their activity crystallized in a July 1976 Ansar-inspired coup attempt. Government soldiers quickly restored order by killing more than 700 rebels in Khartoum and arresting scores of dissidents, including many prominent religious leaders. Despite this unrest, in the 1977 Presidential election Sudanese voters reelected Nimeiri for a second six-year term as president.

National Reconciliation

Following the 1976 coup attempt, Nimeiri and his opponents adopted more conciliatory policies. In early 1977, government officials met with the National Front in London, and arranged for a conference between Nimeiri and Sadiq al Mahdi in Port Sudan. In what became known as the "national reconciliation," the two leaders signed an eight-point agreement that readmitted the opposition to national life in return for the dissolution of the National Front. The agreement also restored civil liberties, freed political prisoners, reaffirmed Sudan's nonaligned foreign policy, and promised to reform local government. As a result of the reconciliation, the government released about 1,000 detainees and granted an amnesty to Sadiq al Mahdi. The SSU also admitted former supporters of the National Front to its ranks. Sadiq renounced multiparty politics and urged his followers to work within the regime's one-party system.

The first test of national reconciliation occurred during the February 1978 People's Assembly elections. Nimeiri authorized returning exiles who had been associated with the old Umma Party, the Democratic Unionist Party, and the Muslim Brotherhood to stand for election as independent candidates. These independents won 140 of 304 seats, leading many observers to applaud Nimeiri's efforts to democratize Sudan's political system. However, the People's Assembly elections marked the beginning of further political decline. The SSU's failure to sponsor official candidates weakened party discipline and prompted many assembly deputies who also were SSU members to claim that the party had betrayed them. As a result, an increasing number of assembly deputies used their offices to advance personal rather than national interests.

During this time, Nimeiri moved closer to Islamism. Hassan al-Turabi, an Islamist leader who had been imprisoned and exiled after Nimeiri's coup in 1969, was invited back into the country and was promoted to Justice Minister in 1979.

The end of the SSU's political monopoly, coupled with rampant corruption at all levels of government, cast increasing doubt on Nimeiri's ability to govern Sudan. To preserve his regime, Nimeiri adopted a more dictatorial leadership style. He ordered the State Security Organisation to imprison without trial thousands of opponents and dissidents. Nimeiri also dismissed or transferred any minister or senior military officer who appeared to be developing his own power base. Nimeiri selected replacements based on their loyalty to him rather than on their abilities. This strategy caused the president to lose touch with popular feeling and the country's deteriorated political situation.

On June 5, 1983, Nimeiri sought to counter the south's growing political power by redividing the Southern Region into the three old provinces of Bahr al Ghazal, Al Istiwai, and Aali an Nil; he had suspended the Southern Regional Assembly almost two years earlier. The southern-based Sudanese People's Liberation Movement (SPLM) and its military wing, the Sudanese People's Liberation Army (SPLA), which emerged in mid-1983, unsuccessfully opposed this redivision and called for the creation of a new united Sudan.

Within a few months, in September 1983 Nimeiri proclaimed the Sharia as the basis of the Sudanese legal system. Nimeiri's decrees, which became known as the September Laws, were bitterly resented both by secularized Muslims and by the predominantly non-Muslim southerners. Even some conservative Muslims were suspicious of morality laws that banned, for example, "attempted adultery" as they felt there was no Islamic basis for it.(source Mansur Khalid) The SPLM denounced the sharia and the executions and amputations ordered by religious courts. Meanwhile, the security situation in the south had deteriorated so much that by the end of 1983 it amounted to a resumption of the civil war.

In early 1985, anti-government discontent resulted in a general strike in Khartoum. Demonstrators opposed rising food, gasoline, and transport costs. The general strike paralyzed the country. Nimeiri, who was on a visit to the United States, was unable to suppress the rapidly growing demonstrations against his regime. A bloodless military coup led by his defense minister Gen. Abdel Rahman Swar al-Dahab ousted him from power. At the subsequent elections the pro-Islamist leader Sadiq al-Mahdi (who had attempted a coup against Nimeiry in 1976) became Prime Minister.

Second Sudanese Civil War

The Second Sudanese Civil War was a conflict from 1983 to 2005 between the central Sudanese government and the Sudan People's Liberation Army. It was largely a continuation of the First Sudanese Civil War of 1955 to 1972. Although it originated in southern Sudan, the civil war spread to the Nuba mountains and Blue Nile. It lasted for 22 years.

Roughly two million people have died as a result of war, famine and disease caused by the conflict. Four million people in southern Sudan have been displaced at least once (and often repeatedly) during the war. The civilian death toll is one of the highest of any war since World War II.The conflict officially ended with the signing of a peace agreement in January 2005.

Background and causes

The war is often characterized as a fight between the central government expanding and dominating peoples of the periphery, raising allegations of marginalization. Kingdoms and great powers based along the Nile River have fought against the people of inland Sudan for centuries. Since at least the 17th century, central governments have attempted to regulate and exploit the undeveloped southern and inland Sudan.

Some paint the conflict as racial (Arabs in the central government vs. Africans in the South) or as religious (Muslims vs. Christians and Traditional African Religions). Scholars such as Douglas Johnson have pointed at exploitative governance as the root cause.

When the British governed Sudan as a colony they administered the northern and southern provinces separately. The south was held to be more similar to the other east-African colonies — Kenya, Tanganyika, and Uganda — while northern Sudan was more similar to Arabic-speaking Egypt. Northern Arabs were prevented from holding positions of power in the Catholic-dominated south, and trade was discouraged between the two areas. However, in 1946, the British gave in to northern pressure to integrate the two areas. Arabic was made the language of administration in the south, and northerners began to hold positions there. The southern elite, trained in English, resented the change as they were kept out of their own government.[6] After decolonization most power was given to the northern elites based in Khartoum, causing unrest in the south. The British moved towards granting Sudan independence, they failed to consider southern needs. Southern Sudanese leaders weren't even invited to negotiations during the transitional period in the 1950s. In the post-colonial government of 1953, the Sudanization Committee only included 6 southern leaders, though there were some 800 available senior administrative positions.

In the early Sudanese state, the government enacted many repressive measures. In 1962, foreign Christian missionaries were expelled from the country, and Christian schools were closed. The government's attacks on southern protesters resulted in sporadic fighting and mutinies, transitioning into a full-scale civil war. The civil war ended in 1972, with the Addis Ababa Agreement. Part of the agreement was a great deal of religious and cultural autonomy to the south.

Another factor in the second war were the natural resources of Sudan, particularly in the South, where there are significant oil fields. Oil revenues make up about 70% of Sudan's export earnings. Due to numerous tributaries of the Nile river and heavier precipitation in southern Sudan, the south also has greater access to water, and is therefore much more fertile. The north of the country is on the edge of the Sahara desert. The northern desire to control these resources in 2004 to present, and the southern desire to maintain control of the resources where they live, contributed to the war. A parallel war between the Nuer and Dinka also raged in the south.

Government marginalization was also the cause of spreading the war to other regions of Sudan. The government's policy was of taking land from farmers (Muslims and non-Muslims alike) and transferring it to government officials and merchants. This had drastic effects on the population of Darfur and Blue Nile. Eventually this would create unrest all over Sudan, including the north.

Civil war

Before 1985

Addis Ababa Agreement ended

The Addis Ababa Accords were incorporated in the Constitution of Sudan; the violation of the agreement led to the second civil war.

The first violations occurred when President Gaafar Nimeiry attempted to take control of oil fields straddling the north-south border. Oil had been discovered in Bentiu in 1978, in southern Kurdufan and Upper Blue Nile in 1979, the Unity oilfields in 1980 and Adar oilfields in 1981, and in Heglig in 1982. Access to the oil fields meant significant economic benefit to whoever controlled them.

Islamic fundamentalists in the north had been discontented with the Addis Ababa Agreement, which gave relative autonomy to the non-Islamic majority Southern Sudan Autonomous Region. The fundamentalists continued to grow in power, and in 1983 President Nimeiry declared all Sudan an Islamic state, terminating the Southern Sudan Autonomous Region.

Sudan People's Liberation Army (SPLA)

The Sudan People's Liberation Army (SPLA) was founded in 1983 as a rebel group, to reestablish an autonomous Southern Sudan by fighting against the central government. While based in Southern Sudan, it identified itself as a movement for all oppressed Sudanese citizens, and was led by John Garang. Initially, the SPLA campaigned for a "United Sudan", criticizing the central government for policies that were leading to national "disintegration".

In September 1984, President Nimeiry announced the end of the state of emergency and dismantled the emergency courts but soon promulgated a new judiciary act, which continued many of the practices of the emergency courts. Despite Nimeiry's public assurances that the rights of non-Muslims would be respected, southerners and other non-Muslims remained deeply suspicious.

1985–1991

On 6 April, senior military officers led by Gen. Abdul Rahman Suwar ad-Dahhab mounted a coup. Among the first acts of the new government was to suspend the 1983 constitution, rescind the decree declaring Sudan's intent to become an Islamic state, and disband Nimeiry's Sudan Socialist Union. However, the "September laws" instituting Islamic Sharia law were not suspended.

A 15-member transitional military council was named, chaired by Gen. Suwar ad-Dahhab, in 1983. In consultation with an informal conference of political parties, unions, and professional organizations—known as the "Gathering"—the military council appointed an interim civilian cabinet, headed by Prime Minister Dr. Al-Jazuli Daf'allah. Elections were held in April 1986, and a transitional military council turned over power to a civilian government as promised. The government was headed by Prime Minister Sadiq al-Mahdi of the Umma Party. It consisted of a coalition of the Umma Party, the Democratic Unionist Party (DUP) (formerly the NUP-National Unionist Party), the National Islamic Front (NIF) of Hassan al-Turabi, and several southern region parties. This coalition dissolved and reformed several times over the next few years, with Prime Minister Sadiq al-Mahdi and his Umma Party always in a central role.

Negotiation and escalation

In May 1986, the Sadiq al-Mahdi government coalition began peace negotiations with the Sudan People's Liberation Army (SPLA) led by Col. John Garang. In that year the SPLA and a number of Sudanese political parties met in Ethiopia and agreed to the "Koka Dam" declaration, which called for abolishing Islamic Sharia law and convening a constitutional conference. In 1988, the SPLA and the DUP agreed on a peace plan calling for the abolition of military pacts with Egypt and Libya, freezing of Sharia law, an end to the state of emergency, and a cease-fire. However during this period the second civil war intensified in lethality, and the national economy continued to deteriorate. When prices of basic goods were increased in 1988, riots ensued, and the price increases were cancelled. When Prime Minister Sadiq al-Mahdi refused to approve a peace plan reached by the Democratic Unionist Party (DUP) and the Sudan People's Liberation Army (SPLA) in November 1988, the DUP left the government. The new government consisted essentially of the Umma Party and the fundamentalist National Islamic Front (NIF).

In February 1989, the army presented Prime Minister Sadiq al-Mahdi with an ultimatum: he could move toward peace or be removed. He chose to form a new government with the DUP, and approved the SPLA/DUP peace plan. A constitutional conference was tentatively planned for September 1989.

Revolutionary Command Council for National Salvation

On 30 June 1989, however, military officers under then Col. Omar Hassan al-Bashir, with National Islamic Front (NIF) instigation and support, replaced the Sadiq al-Mahdi government with the Revolutionary Command Council for National Salvation (RCC), a military junta of 15 military officers (reduced to 12 in 1991) assisted by a civilian cabinet. As General al-Bashir he became: president; chief of state; prime minister; and chief of the armed forces.

The new RCC al-Bashir military government banned trade unions, political parties, and other "non-religious" institutions. 78,000 members of the army, police, and civil administration were purged in order to reshape the government.

Criminal Act of 1991

In March 1991, a new penal code, the Criminal Act of 1991, instituted harsh punishments nationwide, including amputations and stoning. Although the southern states were officially exempt from these Islamic prohibitions and penalties, the 1991 act provided for a possible future application of Islamic Shari’a law in the south. In 1993, the government transferred most non-Muslim judges from the south to the north, replacing them with Muslim judges in the south.[9] The introduction of Public Order Police to enforce Shari’a law resulted in the arrest, and treatment under Shari’a penalties, of southerners and other non-Muslims living in the north.

Conduct of the war: 1991–2001

The Sudan People's Liberation Army (SPLA) was in control of large areas of Equatoria, Bahr al Ghazal, and Upper Nile provinces and also operated in the southern portions of Darfur, Kordofan, and Blue Nile provinces. The government controlled a number of the major southern towns and cities, including Juba, Wau, and Malakal. An informal cease-fire in May broke down in October 1989.

In July 1992, a government offensive seized southern Sudan, and captured the SPLA headquarters in Torit.

It is estimated that as many as 200,000 Southern Sudanese and Nuba children and women have been taken into slavery from Southern Sudanese towns and villages during the war. Both the government regular armed forces and notorious militia (known as the People's Defense Forces, PDF) were used to attack and raid villages in the South and the Nuba Mountains for slaves and cattle.

SPLA dissension

In August 1991, internal dissension among the rebels led opponents of Colonel Garang's leadership of the SPLA to form the so-called Nasir faction of the SPLA rebel army. The attempt to overthrow Garang was led by Riek Machar and Lam Akol. In September 1992, William Nyuon Bany formed a second rebel faction, and in February 1993, Kerubino Kwanyin Bol formed a third rebel faction. On 5 April 1993, the three dissident rebel factions announced a coalition of their groups called SPLA United at a press conference in Nairobi, Kenya. Yet Sudan’s national governments have a long history of using proxies in Southern Sudan, and the North–South border areas, to fight their wars and preserve their regular forces. These militias were recruited locally, and with covert ties to the national government. Many of the Khartoum-aligned groups were created and then armed by the NIF in a deliberate ‘divide and rule’ strategy.

After 1991, the factions clashed occasionally and thus, the rebels lost much of their credibility with the West.

Sudanese alignments

Then, in 1990–91, the Sudanese government supported Saddam Hussein in the Gulf War. This changed American attitudes toward the country. Bill Clinton's administration prohibited American investment in the country and supplied money to neighbouring countries to repel Sudanese incursions. The US also began attempts to "isolate" Sudan and began referring to it as a rogue state.

Since 1993, the leaders of Eritrea, Ethiopia, Uganda, and Kenya have pursued a peace initiative for Sudan under the auspices of the Intergovernmental Authority on Development (IGAD), but results have been mixed. Despite that record, the IGAD initiative promulgated the 1994 Declaration of Principles (DOP) that aimed to identify the essential elements necessary to a just and comprehensive peace settlement; i.e., the relationship between religion and the state, power-sharing, wealth-sharing, and the right of self-determination for the south. The Sudanese Government did not sign the DOP until 1997 after major battle field losses to the SPLA.

SPLA alignments

In 1995, the opposition in the north united with parties from the south to create a coalition of opposition parties called the National Democratic Alliance. This development opened a northeastern front to the civil war, making it more than before a center-periphery rather than simply a north-south conflict. The SPLA, DUP, and Umma Parties were the key groups forming the NDA, along with several smaller parties and northern ethnic groups.

In 1995, Eritrea, Ethiopia and Uganda stepped up their military assistance to the SPLA to the point of sending active troops into Sudan. Eritrean and Ethiopian military involvement weakened when the two countries entered a border conflict in 1998. Uganda's support weakened when it shifted its attention to the conflict in the Democratic Republic of Congo.

By 1997, seven groups in the government camp, led by former Garang lieutenant Riek Machar, signed the Khartoum Peace Agreement with the NIF, thereby forming the largely symbolic South Sudan Defence Forces (SSDF) umbrella. Also in 1997, the government signed the Nuba Mountains, and Fashoda agreements with rebel factions. These included the Khartoum, agreements that ended military conflict between the government and significant rebel factions. Many of those leaders then moved to Khartoum where they assumed marginal roles in the central government, or collaborated with the government in military engagements against the SPLA. These three agreements paralleled the terms and conditions of the IGAD agreement, calling for a degree of autonomy for the south and the right of self-determination.

In July 2000, the Libyan/Egyptian Joint Initiative on the Sudan was mooted, calling for the establishment of an interim government, power-sharing, constitutional reform, and new elections. Southern critics objected to the joint initiative because it neglected to address issues of the relationship between religion and the state and failed to mention the right of self-determination. It is unclear to what extent this initiative will have a significant impact on the search for peace, as some critics view it as more aimed at a resolution among northern political parties and protecting the perceived security interests of Egypt in favour of the unity of the Sudan.

Peace agreement

Peace talks between the southern rebels and the government made substantial progress in 2003 and early 2004, although skirmishes in parts of the south continued. A Comprehensive Peace Agreement was signed on 9 January 2005 in Nairobi.

The terms of the peace treaty were:

      - The south had autonomy for six years, followed by a referendum on independence (the Southern Sudanese independence referendum, 2011).

      - Both sides of the conflict would have merged portions of their armed forces into a 39,000-strong force after six years (the Joint Integrated Units), if the Southern Sudanese independence referendum had turned out against secession.

   - Oil revenues were divided equally between the government and SPLA during the six-year autonomy period.

   -Jobs were split according to varying ratios (central administration: 70 to 30, Abyei/Blue Nile State/Nuba Mountains: 55 to 45, both in favour of the government).

   -Islamic Sharia law was applied in the north, while terms of use of Sharia in the south were decided by the elected assembly.

The status of three central and eastern provinces was a point of contention in the negotiations.

Politics of Sudan (1986–present)

In June 1986, Sadiq al Mahdi formed a coalition government with the Umma Party, the Democratic Unionist Party (DUP), the National Islamic Front (NIF), and four southern parties. Unfortunately, however, Sadiq proved to be a weak leader and incapable of governing Sudan. Party factionalism, corruption, personal rivalries, scandals, and political instability characterized the Sadiq regime. After less than a year in office, Sadiq al Mahdi dismissed the government because it had failed to draft a new penal code to replace the sharia, reach an agreement with the IMF, end the civil war in the south, or devise a scheme to attract remittances from Sudanese expatriates. To retain the support of the DUP and the southern political parties, Sadiq formed another ineffective coalition government.

Second coalition

Instead of removing the ministers who had been associated with the failures of the first coalition government, Sadiq al Mahdi retained thirteen of them, of whom eleven kept their previous portfolios. As a result, many Sudanese rejected the second coalition government as being a replica of the first. To make matters worse, Sadiq and DUP leader Muhammad Uthman al Mirghani signed an inadequate memorandum of understanding that fixed the new government's priorities as affirming the application of the sharia to Muslims, consolidating the Islamic banking system, and changing the national flag and national emblem. Furthermore, the memorandum directed the government to remove former leader Nimeiri's name from all institutions and dismiss all officials appointed by Nimeiri to serve in international and regional organizations. As expected, antigovernment elements criticized the memorandum for not mentioning the civil war, famine, or the country's disintegrating social and economic conditions.

In August 1987, the DUP brought down the government because Sadiq al Mahdi opposed the appointment of a DUP member, Ahmad as Sayid, to the Supreme Commission. For the next nine months, Sadiq and Mirghani failed to agree on the composition of another coalition government. During this period, Sadiq moved closer to the NIF. However, the NIF refused to join a coalition government that included leftist elements. Moreover, Turabi indicated that the formation of a coalition government would depend on numerous factors, the most important of which were the resignation or dismissal of those serving in senior positions in the central and regional governments, the lifting of the state of emergency reimposed in July 1987, and the continuation of the Constituent Assembly.

Third coalition

Because of the endless debate over these issues, it was not until May 15, 1988, that a new coalition government emerged headed by Sadiq al Mahdi. Members of this coalition included the Umma, the DUP, the NIF, and some southern parties. As in the past, however, the coalition quickly disintegrated because of political bickering among its members. Major disagreements included the NIF's demand that it be given the post of commissioner of Khartoum, the inability to establish criteria for the selection of regional governors, and the NIF's opposition to the replacement of senior military officers and the chief of staff of the executive branch.

In November 1988, another more explosive political issue emerged when Mirghani and the SPLM signed an agreement in Addis Ababa that included provisions for a cease-fire, the freezing of the sharia, the lifting of the state of emergency, and the abolition of all foreign political and military pacts. The two sides also proposed to convene a constitutional conference to decide Sudan's political future. The NIF opposed this agreement because of its stand on the sharia. When the government refused to support the agreement, the DUP withdrew from the coalition. Shortly thereafter armed forces commander in chief Lieutenant General Fathi Ahmad Ali presented an ultimatum, signed by 150 senior military officers, to Sadiq al Mahdi demanding that he make the coalition government more representative and that he announce terms for ending the civil war.

End of al Mahdi rule

On March 11, 1989, Sadiq al Mahdi responded to this pressure by dissolving the government. The new coalition had included the Umma, the DUP, and representatives of southern parties and the trade unions. The NIF refused to join the coalition because it was not committed to enforcing the sharia. Sadiq claimed his new government was committed to ending the southern civil war by implementing the November 1988 DUP-SPLM agreement. He also promised to mobilize government resources to bring food relief to famine areas, reduce the government's international debt, and build a national political consensus.

Sadiq's inability to live up to these promises eventually caused his downfall. On June 30, 1989, Colonel (later Lieutenant General) Umar Hassan Ahmad al Bashir overthrew Sadiq and established the Revolutionary Command Council for National Salvation to rule Sudan. Bashir's commitment to imposing the sharia on the non-Muslim south and to seeking a military victory over the SPLA, however, seemed likely to keep the country divided for the foreseeable future and hamper resolution of the same problems faced by Sadiq al Mahdi. Moreover, the emergence of the NIF as a political force made compromise with the south more unlikely.

The Revolutionary Command Council dissolved itself in October 1993. Its powers were devolved to the President (al Bashir declared himself the President) and the Transitional National Assembly.

Conflict in the south, Darfur conflict and conflict with Chad

The civil war in the south has displaced more than 4 million southerners. Some fled into southern cities, such as Juba; others trekked as far north as Khartoum and even into Ethiopia, Kenya, Uganda, Egypt, and other neighboring countries. These people were unable to grow food or earn money to feed themselves, and malnutrition and starvation became widespread. The lack of investment in the south resulted as well in what international humanitarian organizations call a “lost generation” who lack educational opportunities, access to basic health care services, and little prospects for productive employment in the small and weak economies of the south or the north.

In early 2003 a new rebellion of Sudan Liberation Movement/Army (SLM/A) and Justice and Equality Movement (JEM) groups in the western region of Darfur began. The rebels accused the central government of neglecting the Darfur region, although there is uncertainty regarding the objectives of the rebels and whether they merely seek an improved position for Darfur within Sudan or outright secession. Both the government and the rebels have been accused of atrocities in this war, although most of the blame has fallen on Arab militias (Janjaweed) allied with the government. The rebels have alleged that these militias have been engaging in ethnic cleansing in Darfur, and the fighting has displaced hundreds of thousands of people, many of them seeking refuge in neighboring Chad. There are various estimates on the number of human casualties, ranging from under twenty thousand to several hundred thousand dead, from either direct combat or starvation and disease inflicted by the conflict.

In 2004 Chad brokered negotiations in N'Djamena, leading to the April 8 Humanitarian Ceasefire Agreement between the Sudanese government, the JEM, and the SLA. However, the conflict continued despite the ceasefire, and the African Union (AU) formed a Ceasefire Commission (CFC) to monitor its observance. In August 2004, the African Union sent 150 Rwandan troops in to protect the ceasefire monitors. It, however, soon became apparent that 150 troops would not be enough, so they were joined by 150 Nigerian troops.

On September 18, 2004 United Nations Security Council issued Resolution 1564 declaring that the government of Sudan had not met its commitments, expressing concern at helicopter attacks and assaults by the Janjaweed militia against villages in Darfur. It welcomed the intention of the African Union to enhance its monitoring mission in Darfur and urged all member states to support such efforts. During 2005 the African Union Mission in Sudan force was increased to about 7,000.

The Chadian-Sudanese conflict officially started on December 23, 2005, when the government of Chad declared a state of war with Sudan and called for the citizens of Chad to mobilize themselves against Rally for Democracy and Liberty (RDL) militants (Chadian rebels backed by the Sudanese government) and Sudanese militiamen who attacked villages and towns in eastern Chad, stealing cattle, murdering citizens, and burning houses.

Peace talks between the southern rebels and the government made substantial progress in 2003 and early 2004, although skirmishes in parts of the south have reportedly continued. The two sides have agreed that, following a final peace treaty, southern Sudan will enjoy autonomy for six years, and after the expiration of that period, the people of southern Sudan will be able to vote in a referendum on independence. Furthermore, oil revenues will be divided equally between the government and rebels during the six-year interim period. The ability or willingness of the government to fulfill these promises has been questioned by some observers, however, and the status of three central and eastern provinces was a point of contention in the negotiations. Some observers wondered whether hard line elements in the north would allow the treaty to proceed.

A final peace treaty was signed on 9 January 2005 in Nairobi. The terms of the peace treaty are as follows:

    The south will have autonomy for six years, followed by a referendum on secession.

    Both sides of the conflict will merge their armed forces into a 39,000-strong force after six years, if the secession referendum should turn out negative.

    Income from oilfields is to be shared evenly between north and south.

    Jobs are to be split according to varying ratios (central administration: 70 to 30, Abyei/Blue Nile State/Nuba mountains: 55 to 45, both in favour of the government).

    Islamic law is to remain in the north, while continued use of the sharia in the south is to be decided by the elected assembly.

On 31 August 2006, the United Nations Security Council approved Resolution 1706 to send a new peacekeeping force of 17,300 to Darfur. In the following months, however, UNMIS was not able to deploy to Darfur due to the Government of the Sudan’s steadfast opposition to a peacekeeping operation undertaken solely by the United Nations. The UN then embarked on an alternative, innovative approach to try to begin stabilize the region through the phased strengthening of AMIS, before transfer of authority to a joint African Union/United Nations peacekeeping operation. Following prolonged and intensive negotiations with the Government of the Sudan and significant international pressure, the Government of the Sudan finally accepted the peacekeeping operation in Darfur.

In 2009 the International Criminal Court issued an arrest warrant for al-Bashir, accusing him of crimes against humanity and war crimes.

In 2009 and 2010 a series of conflicts between rival nomadic tribes in South Kordofan caused a large number of casualties and displaced thousands.

An agreement for the restoration of harmony between Chad and Sudan, signed January 15, 2010, marked the end of a five-year war between them.

The Sudanese government and the JEM signed a ceasefire agreement ending the Darfur conflict in February, 2010.

In January 2011 referendum on independence for Southern Sudan was held, and the South voted overwhelmingly to secede later that year as the Republic of South Sudan, with its capital at Juba and Kiir Mayardit as its first president. Al-Bashir announced that he accepted the result, but violence soon erupted in the disputed region of Abyei, claimed by both the North and the South.

On June 6, 2011 armed conflict broke out in South Kordofan between the forces of Northern and Southern Sudan, ahead of the scheduled independence of the South on July 9. This followed an agreement for both sides to withdraw from Abyei.On June, 20 the parties agreed to demilitarize the contested area of Abyei where Ethiopian peacekeepers will be deployed.

On July 9, 2011 South Sudan became an independent country.