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Sudan: The Wars That Shaped General Bashir, Museveni Relations

The late 1920s witnessed the rise of the Muslim Brotherhood, whose ideology would later shape the politics of the Middle East and North Africa.

Proponents of Muslim Brotherhood championed the idea of a theocratic state.

The idea was since most African states had witnessed oppression and exploitation during colonialism, there was need to return to a state of purity.

In this case, Islamic states would be run on the principles of Quran and teachings as well as the traditions of Prophet Muhammad.

The Muslim Brotherhood movement had liberal views on slaves, welfare and common prosperity.

These ideals, birthed and nurtured in a small school in Egypt, quickly spread to Syria, Libya, Jordan and also took root in Sudan.

Muslim Brotherhood was quickly embraced by Al-Turabi, the leader of the National Islamic Front (NIF) in Sudan.

Turabi would later embark on ambitious project of spreading the Islamist ideology of theocracy from the source of Nile in Uganda to Egypt.

In the early 1960s, Muslim Brotherhood started placing its cadres in different parts of Sudan’s economy, military, banking sector and political structures. This would create a base for creation of a theocratic state in future.

Gen Bashir was among the Muslim Brotherhood cadres in the military, having joined the armed forces in 1960.

Having graduated from the Sudan Military Academy in Khartoum in 1966, Bashir quickly rose through the ranks to become a paratroop officer.

A well-trained commando, Bashir served in the Egyptian Army during the Yom Kippur War in 1973 against Israel.

He would later serve as Sudan’s military attaché to the United Arab Emirates and later commander of an armoured parachute brigade.

Islamic State

Bashir’s rapid rise in the armed forces and future alliances with Thurabi would spark a costly and bloody war in his country; facilitate the rise of John Garang and trigger the intervention of President Museveni and Ethiopia’s Mengistu Haile Mariam in Sudan politics.

It will be recalled that Jaafar Muhammad an-Nimeiry had earlier in 1969 taken power in a military coup. He initially pursued socialist and Pan-Arabist policies.

In 1972 he signed the Addis Ababa Agreement, ending the First Sudanese Civil War and allowed the South Sudan’s autonomy where by the region would have the Vice President of the Sudan.

He later became an ally of the United States. In the late 1970s he moved towards Islamism, and in 1983 he imposed Sharia law throughout the country.

In violation of the Addis Ababa Agreement he dissolved the southern Sudanese government, thereby prompting a renewal of the civil war, the Second Sudanese Civil War. In 1984 he declared a state of emergency, giving special powers to the military.

Rise of Garang

At the time, John Garang, a youthful activist, was a member of the Anyanya movement in South Sudan. Having studied from Dar es Salaam, Tanzania, Garang had linked up with revolutionaries including President Museveni.

David Mafabi, who worked closely with Garang, told ChimpReports on Tuesday that at the time, “The South of Sudan was still marginalized by Khartoum. Garang didn’t agree with the situation but being among the minority, he continued to serve in Sudan’s armed forces.”

Garang quietly pushed for a united Sudan, saying the ‘Arab North’ was just fiction as Sudan and Egypt were occupied by black people for centuries.

Nevertheless, in 1983, the Anyanyas led a revolt against Nimeiry’s Islamist policies.

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On 6 April 1985, while Nimeiry was on an official visit to the United States of America in the hope of gaining more financial aid from Washington, a bloodless military coup led by his defence minister Gen. Abdel Rahman Swar al-Dahab ousted him from power.

Gen Abdel Rahman became the Chairman of the Transitional Military Council, surrendering power to the government of head of state Ahmed al-Mirghani and Prime Minister Sadiq al-Mahdi in 1986.

Enter Bashir

When he returned to Sudan as a colonel in the Sudanese Army, Bashir led a group of army officers in ousting the unstable coalition government of Prime Sadiq al-Mahdi in a bloodless military coup on 30 June 1989.

Tue to his Muslim Brotherhood ideology, Bashir suspended political parties and introduced an Islamic legal code on the national level.

He also allied himself with Hassan al-Turabi, the leader of the National Islamic Front, who along with al-Bashir began institutionalizing Sharia law in the northern part of Sudan.

Further on, Bashir issued purges and executions of people whom he alleged to be coup leaders in the upper ranks of the army, the banning of associations, political parties, and independent newspapers, as well as the imprisonment of leading political figures and journalists.


Amid this oppression, John Garang led over 3,000 soldiers who had defected from the mainstream Sudan army to launch a war against Sudan Khartoum.

Mafabi recalled that between 1986-1989, SPLA had taken over the Eastern and Western Equatoria.

“The territory Garang controlled was three times bigger than Uganda,” recalled Mafabi, whom we contacted for this special article.

As if this was not scary enough, Garang led lightening mobile assault teams to capture large swathes of land in South Kordofan and Blue Nile.

These military offensives and victory alarmed Khartoum and the Arab world.

The SPLA gained the backing of Libya under Muammar Gaddafi; Uganda led by Yoweri Museveni who had taken power in 1986 and Ethiopia under Mengistu.

Garang’s philosophy of ‘Sudanism’ for secular and multiethnic New Sudan -whereby the people of Sudan would live in cohesion and collectively renounce the identities of Arabness, Black African-ness, Islam or Christianity, excited elites in the North.

Realising that Garang meant business and his military victories threatened the foundation of the Islamic state, the Sudanese ruling class led by Bashir responded by declaring Jihad on SPLA.

At the time, historians say, Garang had an army that was capable of overrunning Khartoum.

All SPLA backers had to be fought and removed from power to preserve a theocratic state in Sudan.


In the spring of 1991, Mengistu Haile Mariam’s regime in Ethiopia was toppled by the Khartoum-backed Ethiopian rebels known as Ethiopian People’s Revolutionary Democratic Front.

Upon the rebels’ seizure of government, they closed all SPLA training camps in Ethiopia and cut off the SPLA’s arms supply, forcing the SPLA to return hundreds of thousands of Sudanese back to South Sudan. This disrupted military operations and leadership within the SPLA.

However, the movement suffered its major setback when the leadership was split.

Shortly after, SPLA faced an internal setback with its top leaders Riek Machar and Lam Akol trying to oust Garang.

Machar’s view was that Garang’s idea of a united Sudan was not achievable given the challenges of the time.

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Pursuing such an objective would lead to an endless protracted war with no end in sight. They had fought for decades and it was time to lay down weapons.

“If they (Sudan North) don’t want us, why do we force ourselves onto them,” Machar argued then.

The SPLA was split, leading to deadly battles in Nasir.

Bashir quickly spotted the weakness in SPLA, hence providing millions of dollars and arms to Machar not only to resist but fight Garang.

Bashir’s divide and rule method worked effectively to derail SPLA’s agenda of a united Sudan.

Machar would as well accept Bashir’s proposal to serve as a conduit of arms and money for LRA’s Joseph Kony, Alice Lakwena and other rebel movements seeking the removal of President Museveni from power.

Enter Museveni

This threatened Museveni’s hold onto power. The rebels which had cropped up after Museveni took power in 1986 had been defeated with many hiding in South Sudan.

Machar, on orders of Bashir, collected and reorganised the rebels to return to Uganda and fight.

Bashir, who was pursuing the Pan-Arab agenda of spreading the Islamist ideology up to the source of the Nile would later face off with Museveni, a battle-hardened fighter who was championing the Pan African cause – having fought in bloody wars that toppled Idi Amin and Milton Obote.

Museveni’s disdain for Muslim Brotherhood can be seen in a speech he read in 2016 at the Sudanese National Dialogue on Land Reform and State Reform in Khartoum.

“I met the former President of Egypt, Mohammed Morsi.  I knew that he had a Party known as the Muslim Brotherhood. I asked him the following question:  Your Excellency, don’t you think that you are endangering your country Egypt by politically exploiting identity in a diverse country like Egypt? You talk of Moslem Brotherhood. In Uganda, the Christians are 86%,” said Museveni.

“What would happen to Uganda if I started talking of “Christian Brotherhood?  What would happen to my 14% Moslems?  What should they do?  Uganda is their only country for which they sacrificed just like the Christians.  It is, obviously provocative.  Mohammed Morsi told me that he would give me the answer next time.  There was to be no next time ─ between me and Mohammed Morsi,” he emphasised.


Meanwhile, Ugandan forces crossed into South Sudan where they pursued and killed rebels. But Kony remained a force to reckon with.

At one moment, an LRA machine gunner was killed by Uganda’s Special Forces. Ugandan forces recovered a gun which UPDF didn’t have.

“We had to ask foreign experts to give us information about the gun recovered from the rebels,” said a retired army officer who preferred anonymity so as to speak freely.

Nevertheless, Museveni continued to support SPLA which inflicted heavy blows on Sudan’s forces.

More rebel movements sprung up in different parts of Sudan, spreading thin Sudan’s military clout.

There also was pressure from the Americans against Sudan for supporting terrorist activities. Sudan had hosted Osama Bin Laden, the founder of Al Qaeda.

In 2005, Bashir agreed to the secession of South Sudan.

“There was new pragmatism on the part of Bashir for purposes of regime survival,” recalled Mafabi.

The South Sudan had created a security buffer for Uganda against Sudan. Khartoum had been hit hard by U.S. sanctions. Bashir could no longer order aerial bombardments of Northern Uganda.

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Uganda was quick to deploy Special Forces when Sudan-backed Machar attempted to overthrow President Salva Kiir in 2013. Ugandan commandos crossed into South Sudan on the night of the coup, securing the army headquarters, presidential palace, airport and vital state installations in a period of 34 hours.

This shocked the Americans in Kampala who had sent a cable to Washington that UPDF needed about three days to mobilise to save Kiir.

Slowly, Bashir was being weakened. Uganda had more influence in South Sudan than Khartoum.

The oil fields stayed in South Sudan much as the pipelines to take the crude oil to the sea remain in the North.

Last moments as president

A few years before his removal from power, Bashir had settled his scores with Museveni. The two leaders played key roles in the stabilization of South Sudan.

Museveni and Bashir exchanged visits. Museveni once traveled to Khartoum where he addressed conferences and attended shooting exercises at Sudan’s military training schools.

Statistics indicate that Sudan imports 20% of Uganda coffee and is the single biggest export market for the product from which about USD100 million is earned.

Museveni told the Uganda-Sudan Business Forum in 2017 that the Government of Uganda is “finalizing efforts to revitalize Uganda Airlines and once operationalised, Khartoum will be one of the Airline’s first destinations.”

Notably, Uganda’s senior army officers and intelligence chiefs spearheaded ‘Operation Goodwill’ that saw 130 Sudanese army officers including a Colonel and civilians freed by SPLM-North.

This was after the collapse of 15 international community-mediated peace talks to have the prisoners released.

The prisoners had been held for about 20 years.

The SPLM-N was founded by organizations of the predominantly South Sudanese Sudan People’s Liberation Movement/Army that remained in Sudan following the South Sudanese vote for independence in 2011.

Residents of South Kordofan and Blue Nile hoped to become citizens of the new nation but were excluded from the peace deal.

Despite the Comprehensive Peace Agreement, a low-level conflict continued in Sudan, with the Movement’s armed branch engaging in an active insurgency against the government of Bashir.

In Uganda, ‘Operation Goodwill’ was kept a top secret known by only President Museveni, former Chief of Defence Forces Gen Katumba Wamala, ex Special Forces Commander (SFC) Gen Muhoozi Kainerugaba, Director General ESO Ambassador Joseph Ochwet, Col. Geoffrey Karugaba of Military Police and Major Allan Matsiko of Special Forces.

This successful operation breathed new life into Uganda’s relations with Sudan.

Way forward

Mafabi, who is a senior presidential advisor on political affairs, expressed hope of better relations between Uganda and Sudan.

“Our principles of Pan Africanism and democracy are intact. We can’t determine what happens in Sudan,” said Mafabi, adding, “Whatever happens, the issues will be resolved. We will relate with any government in Sudan basing on our values. The state-to-state relations will be there.”


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