Khartoum: A ruined capital controlled by Sudan's Islamists

The Battle for Khartoum is not over, it has just entered a new phase. Four months after the Sudanese Armed Forces reoccupied the city, they face a new challenge, expelling the armed groups that have occupied the city since and now hold it as a down payment on the Islamic republic they are determined to establish.

A month ago,  SAF commander General Abdel Fattah al-Burhan reportedly ordered all military formations and armed groups, including those that had allied with the SAF during the fighting against the RSF, to withdraw from Khartoum within two weeks. That looks like a tall order.

The SAF’s retaking of Khartoum relied heavily on a “hotch-potch” array of forces beyond the regular military, assembled through alliances with various militia groups and armed movements after General Burhan lost a great deal of his infantry after the rupture with the RSF. According to an analysis by ACLED, an independent conflict monitoring group, General Burhan is compensated by reportedly recruiting among traditional groups, their armed militias, and other paramilitary groups either formerly neutral or aligned either with the RSF or former President Omar al-Bashir’s regime. Among these groups were the Darfur Joint Forces and the Sudan Shield Forces. Burhan also revived previously dismantled SAF paramilitaries, like the Popular Defence Forces (PDF), al-Baraa Ibn Malik Brigade, and the National Intelligence and Security Service combat troops.

The most significant allied forces include the Al-Bara Ibn Malik Brigade, an Islamist-linked militia that played a key role in the battle for Khartoum. Named after a prominent Muslim fighter from early Islamic conquests, this brigade represents the growing influence of Islamist networks that have mobilised civilian support through popular resistance brigades. The Brigade is central to the SAF's reliance on Islamist allies.

The Sudan Shield Forces, originally created by military intelligence in 2022, initially fought alongside the RSF before defecting to the SAF in October 2024. Additionally, various neighbourhood defence units have emerged in urban areas across Khartoum and, it is alleged, increasingly operate outside SAF oversight, creating profound challenges for SAF command and control.

That has been abundantly clear in the allegedly unlawful killings and detentions across various parts of Khartoum, of which the SAF and its allied armed groups have been accused. Reporting for The New Humanitarian, local freelance journalist Mohammed Amin writes that “videos have circulated on social media showing soldiers in SAF uniforms detaining or killing people suspected of helping the RSF. The label “cooperator” has become a source of fear, and many feel it is used to target anyone critical of the SAF.”

Mohamed Saad, of Charles University in the Czech Republic, told the African Defence Forum: “If the rise of armed groups is not stemmed, Saad says they may evolve and establish territories where local commanders wield unchecked power. This would undermine the possibility of establishing central governance in Sudan. These groups don’t share a single goal. Some fight for self-defence, others for political power. Some for revenue and wealth. Others are seeking ethnic control — Sudan’s population has 56 ethnic groups and 595 sub-ethnic groups. This is what makes Sudan’s war even more dangerous: fragmentation is creating multiple mini-wars within the larger conflict.”

This is the two-headed beast that General Burhan has created by breaking with the RSF in his effort to establish his own hegemony in Sudan: a deeply fragmented array of armed forces, each with their own agendas; and a reliance on Islamist groups that are set on establishing an Islamist regime that is permanently secured in place through armed force. Leaving no room for democracy, a secular state, and the protection of minority ethnic groups and religions, let alone the demilitarisation of Khartoum.

Left to the SAF, which reportedly cannot control the city, Khartoum seems likely to remain, very sadly, a place of fear and oppression for a long time to come.  

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