Sudan's Hidden War: Muslim Brotherhood's Grip on Army Threatens Regional Stability, Global Trade
Sudan's brutal 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, which appears to be using the SAF as a Trojan horse to dominate northeast Africa and the Red Sea, a critical artery for global commerce.
The Muslim Brotherhood, sponsored by Qatar, appears to be hijacking the SAF to stage a takeover, recycling old alliances under new guises. Despite recent concessions to the United States and Egypt, the Muslim Brotherhood's grip in Sudan -- backed by Qatar and Iran -- threatens regional and global stability, potentially including freedom of passage in the Red Sea.
[T]he Muslim Brotherhood — known in Sudan as the Islamic Movement — has entrenched itself in the SAF, and turned it into a tool for their regional ambitions to take control of northeast Africa and the Red Sea.
The Muslim Brotherhood is not just allied with the SAF; individuals in it seem to be steering the SAF to take total control of Sudan in order to make it the Muslim Brotherhood's stronghold in Africa and the Middle East.
The SAF is infiltrated by jihadist factions such as the Al-Bara Bin Malik Brigade (the Muslim Brotherhood's local military arm), the Bunyan Al-Marsous Brigade, and Justice and Equality Movement rebels led by Finance Minister Jibril Ibrahim. These groups, tied to Bashir's ruthless National Intelligence and Security Service, frame their fight as a "jihad" against the RSF, which is backed by the United Arab Emirates and Sudan's secular civil society.
Ali Ahmed Karti, the U.S.-sanctioned Islamic Movement leader, is, as reported by Arab media outlets, 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.
One analyst suggested that the five generals were dismissed after Burhan met with U.S. Special Envoy Mossad Boulos in Switzerland, on August 11, 2025. Researcher Mujahid Ahmed, however, warns that the Muslim Brotherhood's influence persists, extending into civilian institutions, especially the foreign affairs and justice ministries. According to the Ayin Network, Al-Burhan apparently still relies on Karti and Bashir's loyalist, Ahmed Haroun, for battlefield support, indicating a tactical, not total, break.
Iran has been supplying the Muslim Brotherhood-SAF axis with arms, including Ababil-3 and Mohajer-6 drones, which were delivered to Port Sudan in March and June 2024. Satellite imagery viewed by the BBC confirms their presence at a military site near Khartoum. Iran's support of this Muslim Brotherhood-SAF axis, tied to its ambitions to have a presence in the Red Sea, coincides with the Brotherhood's goals: namely, threatening U.S. allies such as Israel, Saudi Arabia and Egypt.
Burhan's "cosmetic" purge of Islamist generals shows that indeed he can be influenced by Egypt and by the United States, but his reliance on the Muslim Brotherhood's financial and military support limits his ability to implement any real reforms.
Sudan is evidently very much a part of the Muslim Brotherhood's global agenda. Ignoring events there will only allow a hostile stronghold to emerge in a region strategically vital for the interests of the West.
Sudan's brutal civil war, often overshadowed by global headlines, 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, which appears to be using the SAF as a Trojan horse to dominate northeast Africa and the Red Sea, a critical artery for global commerce.
Despite recent moves by SAF leader General Abdel Fattah Al-Burhan to curb Islamist influence, presumably at the request of the United States or Egypt, the efforts of the Muslim Brotherhood, which has deep roots in his army, to achieve control of Sudan, northeast Africa and the Red Sea, signal a dangerous threat that could disrupt oil supplies, inflate global prices, and revive Sudan as a terrorist hub, imperiling Western interests.
The Muslim Brotherhood, sponsored by Qatar, appears to be hijacking the SAF to stage a takeover, recycling old alliances under new guises. Despite recent concessions to the United States and Egypt, the Muslim Brotherhood's grip in Sudan -- backed by Qatar and Iran -- threatens regional and global stability, potentially including freedom of passage in the Red Sea. The U.S. would do well to intensify sanctions, diplomatic pressure, and support regional actors in efforts to dismantle these networks.
The Muslim Brotherhood's influence is increasingly recognized as a global threat by governments in countries such as the United States and France. A May 21, 2025 report requested by the French government on the Muslim Brotherhood's role in France and Europe, detailed the threats posed by the Islamist movement shaping "parallel Islamic ecosystems," challenging Western secular values.
A Legacy of Islamist Control
Sudan's descent into chaos began in 1989, when General Omar Al-Bashir, backed by the Muslim Brotherhood's National Islamic Front, seized power. For three decades, his regime orchestrated genocides in South Sudan and Darfur, sheltered Osama bin Laden from 1992 to 1997, and enabled Al-Qaeda's attacks, including the 1998 U.S. Embassy bombings in Kenya and Tanzania. Bashir's regime also funneled Iranian missiles to Hamas in the Gaza Strip, and supported Lord's Resistance Army in Uganda, making Sudan a global extremist stronghold.
The 2019 ouster of Al-Bashir had sparked hopes for democracy, but Burhan's 2021 coup against the transitional government and the 2023 war with the RSF, which wanted to defeat Burhan and his Muslim Brotherhood allies and take over the country, crushed those dreams. Beneath the surface, the Muslim Brotherhood — known in Sudan as the Islamic Movement — has entrenched itself in the SAF, and turned it into a tool for their regional ambitions to take control of northeast Africa and the Red Sea.
The Muslim Brotherhood is not just allied with the SAF; individuals in it seem to be steering the SAF to take total control of Sudan in order to make it the Muslim Brotherhood's stronghold in Africa and the Middle East.
Sudan, at the crossroads of Sub-Saharan Africa and the Middle East, happens to be in an extremely critical strategic position. It has access to the Red Sea and vital trade routes such as the Suez Canal, and is also a crucial transit point for migrants traveling from the Horn of Africa and the Sahel to North Africa, then on to Europe.
The SAF is infiltrated by jihadist factions such as the Al-Bara Bin Malik Brigade (the Muslim Brotherhood's local military arm), the Bunyan Al-Marsous Brigade, and Justice and Equality Movement rebels led by Finance Minister Jibril Ibrahim. These groups, tied to Bashir's ruthless National Intelligence and Security Service, frame their fight as a "jihad" against the RSF, which is backed by the United Arab Emirates and Sudan's secular civil society.
Social media videos show the Al-Bara Bin Malik Brigade, in Omdurman, halting RSF advances and bolstering SAF operations in Khartoum. A retired officer told the media that Islamic extremists have filled critical infantry gaps. Ali Ahmed Karti, the U.S.-sanctioned Islamic Movement leader, is, as reported by Arab media outlets, 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.
Reports in the Saudi newspaper Asharq Al-Awsat reveal that after 1989, the leadership of the Muslim Brotherhood in Sudan, which was aligned with the Bashir government, purged thousands of non-fundamentalist officers, assassinating some, and took control of admissions to the Military Colleges. By 2019, the SAF was ideologically aligned with the Muslim Brotherhood.
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 also unleashed jihadist battalions, which were rebranded as Burhan's "Popular Resistance."
This summer, there seemed to be cracks in the alliance between the SAF and the Muslim Brotherhood. In August, 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. One analyst suggested that the five generals were dismissed after Burhan met with U.S. Special Envoy Mossad Boulos in Switzerland, on August 11, 2025. Researcher Mujahid Ahmed, however, warns that the Muslim Brotherhood's influence persists, extending into civilian institutions, especially the foreign affairs and justice ministries. According to the Ayin Network, Al-Burhan apparently still relies on Karti and Bashir's loyalist, Ahmed Haroun, for battlefield support, indicating a tactical, not total, break.
Iran's Arms and Qatar's Role
Iran has been supplying the Muslim Brotherhood-SAF axis with arms, including Ababil-3 and Mohajer-6 drones, which were delivered to Port Sudan in March and June 2024. Satellite imagery viewed by the BBC confirms their presence at a military site near Khartoum. Iran's support of this Muslim Brotherhood-SAF axis, tied to its ambitions to have a presence in the Red Sea, coincides with the Brotherhood's goals: namely, threatening U.S. allies such as Israel, Saudi Arabia and Egypt.
Why It Matters to the West
The Red Sea handles 10-15% of the world's maritime commerce, including vital oil and gas shipments. In a conflict, the Muslim Brotherhood-controlled Sudan, using the SAF as a proxy, could choke this route as the Houthis have been doing, thereby spiking prices and impairing American and other economies. The Muslim Brotherhood's ties to Al-Qaeda and the Islamic State risk turning Sudan into a terrorist base targeting Western and allied Middle Eastern interests.
Trump's Sudan Gamble
The Trump administration is navigating a tightrope, trying, it seems, to balance Egypt's pro-SAF stance and UAE's RSF support. Egypt is actively supporting the SAF to bolster its stability as a national institution, while simultaneously trying to curb the influence of the Muslim Brotherhood and its sponsor, Qatar. Ayin Network noted that Egypt insists "the SAF must remain central to any post-war political order," while the UAE requests the opposite. Burhan's "cosmetic" purge of Islamist generals shows that indeed he can be influenced by Egypt and by the United States, but his reliance on the Muslim Brotherhood's financial and military support limits his ability to implement any real reforms.
A Global Wake-Up Call
Sudan is evidently very much a part of the Muslim Brotherhood's global agenda. Ignoring events there will only allow a hostile stronghold to emerge in a region strategically vital for the interests of the West.
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