Civil war between 1989- DEC 2004

General John Garang
After a year of military rule, Sadiq al-Mahdi, the great grandson of Muhammad Ahmad, was elected prime minister in the first free election in 18 years. Voting was postponed in 37 southern constituencies, however, due to a guerrilla war led by southern rebels known as the Sudanese People's Liberation Army (SPLA) against the Muslim Arab government. The newly elected assembly was to draft and approve a new constitution and to hold elections every four years. However, severe food shortages, guerrilla unrest, a mounting debt crisis, and other problems weakened the government's power.
In June 1989 a military coup headed by Brigadier Omar Hassan al-Bashir toppled the Mahdi government. A state of emergency was imposed, and Sudan as ruled through a 15-member Revolutionary Command Council for National Salvation. Conditions deteriorated in the early 1990s, as the Bashir regime suppressed political opposition and stepped up the war against non-Muslim rebels in the south.
In 1993 Bashir took tentative steps toward multiparty democracy, including the dissolution of the military government, but the decision to retain most of his former ministers prompted many to perceive these changes as largely cosmetic.
In January 1994 about 100,000 refugees fled to Uganda when Sudanese troops led an offensive against the SPLA. In March safety zones were established for the transportation of provisions and relief workers to the war-torn south. Throughout 1994 mediators from the Intergovernmental Authority on Drought and Development (IGADD), consisting of representatives from Kenya, Uganda, Ethiopia, and Eritrea, attempted to negotiate a peace agreement between the Sudanese government and the SPLA.
In September the negotiations resulted in the creation of the Supreme Council for Peace, an 89-member body with 38 representatives from the rebel-dominated south. In March 1995 former United States president Jimmy Carter moderated a two-month cease-fire in an effort to allow relief workers to treat cases of river blindness and guinea worm disease in the south. The SPLA resumed its attack in July.

HASSAN AL-TURABI As the leader of Sudan's National Islamic Front, Hassan al-Turabi helped mold Sudan into a fundamental Islamist state after the coup that brought Omar al-Bashir to power in 1989.
Under Bashir, Turabi became speaker of the National Assembly and had a great deal of influence over the government. In the late 1990s a power struggle developed between the two leaders, and in 2000 Bashir stripped Turabi of his powers.
In March 1996 Bashir and his supporters swept presidential and legislative elections. Hassan al-Turabi, the head of a powerful Islamic fundamentalist movement called the National Islamic Front and a national spiritual leader, was elected to the National Assembly and made speaker. In April Sudan faced international condemnation after evidence surfaced linking Bashir's government with a June 1995 assassination attempt on Egyptian president Hosni Mubarak in Ethiopia. In May 1996 the United Nations (UN) levied sanctions against Sudan for refusing to extradite to Ethiopia three suspects in the assassination attempt.
Garang who led SPLA into success died 2 months after swearing in as Sudanese First Vice President and President of the South. He died in a Ugandan jet shortly after a meeting in Kampala.
By the mid-1990s the SPLA, led by John Garang, a former officer in the Sudanese army, controlled most of southern Sudan and a number of important towns. However, the government maintained control over Juba, a large city in the far south, and several key southern towns along the Nile and the main roads. Although several smaller rebel groups have signed peace agreements with the government, the SPLA has stated that it will accept nothing less than complete independence for southern Sudan.
The Sudanese government has accused Ethiopia, Uganda, Eritrea, and Tanzania of aiding the rebels, but these countries have denied the claims. In mid-1998 peace talks, the SPLA and the government tentatively agreed to accept an internationally supervised vote on self-determination in the south. However, no date was set for the vote, and the talks failed to produce a cease-fire.
Peace talks continued, but they repeatedly stalled over major issues such as the government's unwillingness to separate state and religion and disagreement over where the boundary between north and south would lie. Several temporary cease-fires were called during this time in support of the peace effort and to facilitate the delivery of humanitarian aid, including the delivery of food and vaccines, to the war-torn south.

In December 1999 a power struggle between Bashir and Turabi came to a head. Turabi attempted to pass constitutional amendments designed to reduce Bashir's presidential powers by calling for the creation of the office of a prime minister, accountable to the National Assembly, and the removal of presidential control over the selection of state governors. In response to this threat to his authority, Bashir dismissed Turabi and declared a state of emergency, dissolving the National Assembly and suspending parts of the constitution.
Sudan's main opposition parties boycotted December 2000 presidential and legislative elections, criticizing the ongoing state of emergency and the fact that voting would not be held in most southern constituencies. Bashir was reelected with 86.5 percent of the vote and his party, the National Congress Party, won 355 of the 360 seats in the National Assembly.

John Garang being sworn in as Vice President, a step that marked the end of the 20 years war.

The good news of the civil war came in the year of the lord 2004 when President Hassan Al Bashir and the SPLA rebel leader Dr. John Garang signed a permanent ceasefire agreement in Naivasha, Kenya. It was witnessed by Kenyan president Mwai Kibaki and South African president Thambo Mbeki. Another Peace pact ending Africa's longest civil war was signed in Khartoum in January.
 

President Salva Kiir, replaced the late General John Garang. His Vice President Riak Machar launched a war against the SPLA since December 2013.

The pact involved power sharing between the south and the north. Positions in the army and post war rebuilding of southern Sudan.

National Movements and New States in Africa