Sudan’s ongoing civil war is not just a clash between the Sudanese Armed Forces (SAF) and their former military allies-turned rivals, the Rapid Support Forces (RSF). It is a calculated power grab by the Muslim Brotherhood, sponsored by Qatar, which use the SAF as a Trojan horse to dominate Northeast Africa and the Red Sea – a critical artery for global commerce.[1]
Background
On April 15, 2023, the civil war erupted between the SAF, led by Gen. Abdel Fattah Al-Burhan, and the Rapid Support Forces (RSF), commanded by Gen. Mohamed Hamdan Dagalo (known also as “Hemedti”). The RSF quickly gained the upper hand in Khartoum, seizing key sites including the presidential palace and international airport, which forced the SAF government to relocate to Port Sudan. However, momentum shifted dramatically when, on March 21, 2025, the SAF recaptured the presidential palace in Khartoum as part of a sweeping offensive that expelled the RSF from most of the capital by March 26. That marked a pivotal strategic victory for Al-Burhan, who is the Chairman of Sudan’s Sovereignty Council, which reversed nearly two years of RSF entrenchment. As of October 2025, the SAF maintains control of Khartoum.
The SAF as a Trojan Horse of the Muslim Brotherhood
According to international media, in August 2025, Al-Burhan tried to curb Islamist influence, which is deeply rooted in his army. It was reported that, Al-Burhan fired five senior generals who are Islamic extremists, including General Nasreddin, head of the SAF Armored Corps, whom the Muslim Brotherhood had reportedly been grooming as a potential successor to Burhan. Analysts suggested that the five generals were dismissed after Al-Burhan met with U.S. Special Envoy Mossad Boulos in Switzerland, on August 11, 2025. Hence, presumably, the firing came at the request of the United States.[2]
Nevertheless, experts in the Arab world are warning that the Muslim Brotherhood’s influence persists, extending into civilian institutions, especially the foreign affairs and justice ministries.[3] Al-Burhan’s “cosmetic” purge of Islamist generals shows that the West may manage to influence him, but his reliance on the Muslim Brotherhood’s financial, political and military support limits his ability and willingness to implement any reforms.[4]
The SAF is in fact filled with jihadist factions such as the Al-Bara Bin Malik Brigade (the Muslim Brotherhood’s local military arm),[5] the Bunyan Al-Marsous Brigade, and Justice and Equality Movement rebels led by Finance Minister Jibril Ibrahim.[6] These groups, tied to former pro-Muslim Brotherhood president Omar Al-Bashir’s ruthless National Intelligence and Security Service, frame their fight as a “jihad” against the RSF, which is backed by Sudan’s secular civil society.[7]
On October 21, the commander of the Rapid Support Forces, Hemedti, pledged to work on “liberating the Sudanese people from the Muslim Brotherhood organization,” holding the Islamist organization responsible for the continuation of the civil war. He then explained that “elements of the former [Al-Bashir] regime chose the path of war and bloodshed, and they must bear the consequences of their actions.” He added that “those who are fighting today under the banner of the army are in fact Muslim Brotherhood,” stressing that the Islamist organization took “control” over the military institution.[8]
Hemedti further accused Al-Burhan of “deceiving the international community” about the real nature of his relationship with the Muslim Brotherhood.[9]
Back in January, Hemedti explicitly described the Muslim Brotherhood as operating “behind” the SAF and added: “We will pursue the leaders of the Muslim Brotherhood group hiding behind the army, until we liquidate them from the state’s institutions and strip them of power.”[10]
Karti: ‘The Godfather of The Muslim Brotherhood’
Ali Ahmed Karti, the U.S.-sanctioned Islamic Movement leader, is a key orchestrator of the SAF-Muslim Brotherhood alliance. Since his student days, Karti has organized Brotherhood loyalists in the army, and later packed the SAF with jihadists. It was Karti’s ideological influence that apparently derailed the possibility of a civilian-led transitional government in Sudan after the October 2021 military coup. Karti, who served as Minister of Foreign Affairs of Sudan from 2010 to 2015, since June 2021 is the secretary general of the Sudanese Islamic Movement (the name under which the Muslim Brotherhood is known in Sudan), and he is responsible for unleashing jihadist battalions, which were rebranded as Burhan’s “Popular Resistance.” Karti’s networks also fund SAF-aligned Islamist fighters’ salaries via the Sudanese Islamic Movement.[11]
It is worth noting that, after the death of Sudanese Islamist ideologue, Hassan Al-Turabi, Karti managed to become the main Muslim Brotherhood leading figure in Sudan. Sources describe Karti as an “erstwhile loyal supporter” of Al-Turabi and “once a devotee,” highlighting his devotion during Al-Turabi’s peak influence from the late 1980s to the early 2000s.[12]
In January, Hemedti, referred to Karti as the “Godfather of the Muslim Brotherhood,” acting as a “shadow patron” to Burhan, convincing him to steer away from reconciliation and escalate the conflict. Hemedti said: “The godfather of the Muslim Brotherhood group, Ali Karti, has established his military bases inside the army’s headquarters in the city of Omdurman to continue the war against the Rapid Support Forces.” He then added: “We are following you, O Karti, and… we will strip you of power.”[13]
Al-Burhan’s Visit to Qatar
September 16, 2025, on the sidelines of the Arab-Islamic Emergency Summit in Doha, Al-Burhan held a bilateral meeting with the Emir of Qatar, Sheikh Tamim bin Hamad Aal Thani. As reported in the media,[14] Al-Burhan updated the Emir on recent events in Sudan, emphasizing the longstanding historical connections between the Sudanese and Qatari peoples.
In response, Sheikh Tamim reiterated Qatar’s unwavering commitment to the SAF, as a political, military and financial backer.[15] It is worth noting that Qatar directly supplies weapons to the SAF, contributing to its operational capabilities.[16]
Previously, Al-Burhan’s official visits to Doha were made in 2021 and in 2023, in which Qatar pledged continued support.[17] These trips reflect Qatar’s role as a key supporter al-Burhan-led SAF to implement the Muslim Brotherhood’s agenda in Northeast Africa and the Red Sea, which handles 10-15% of the world’s maritime commerce, including vital oil and gas shipments.[18]
Conclusion
As Sudan’s civil war drags into its third year, the Muslim Brotherhood’s insidious entrenchment within the SAF—facilitated by figures like Ali Karti and sustained by Qatari patronage—poses an existential threat to Sudan’s stability and to US interests in the region.
Yet, amid this deepening of the war, Hemedti’s defiant October 21 vow—to “liberate the Sudanese people from the Muslim Brotherhood organization”[19]—resonates as a clarion call for counter Islamist reform. In fact, the war in Sudan is not a mere internal conflict but it is part of a broader battle against the Muslim Brotherhood’s transnational Islamist agenda.
Sudan stands at a precipice: true liberation demands not cosmetic ceasefires, but the decisive uprooting of the Muslim Brotherhood’s grip, which would ensure Sudan’s people reclaim their destiny from the shadows of 1989.[20]
For the West, ignoring these dynamic risks ceding the Northeast Africa and the Red Sea to a Qatari-Brotherhood axis, imperiling trade routes and emboldening extremists from Yemen to Libya and beyond.