By any serious measure, the Sudanese military regime led by General Abdel Fattah al-Burhan does not operate in isolation. At its core lies a deeply entrenched ideological and organizational force: the revolutionaries of the Sudanese Muslim Brotherhood.
While international attention has largely framed Sudan's war as a struggle between the Sudanese Armed Forces (SAF) and the Rapid Support Forces (RSF), this binary obscures a more consequential reality. The conflict is also the latest chapter in the Brotherhood's decades-long project to dominate the Sudanese state — by force when necessary, by infiltration when possible, and by regional alliances when useful.
The Brotherhood as a Wartime Power Broker
Since the outbreak of full-scale war in April 2023, Muslim Brotherhood loyalists have not merely supported the Sudanese army — they have embedded themselves within its operational, intelligence, and political core.
Brotherhood-linked networks mobilized thousands of former intelligence officers, Islamist cadres, and veterans of earlier jihadi campaigns to fight alongside the SAF. These fighters were organized into ideologically driven militias, most prominently the Al-Bara ibn Malik Battalion, alongside formations such as the Shield of the Homeland and North Shield. According to documented reporting, these units received arms, financing, and logistical support through official military channels, blurring the line between state forces and Islamist militias.
Politically, Brotherhood-aligned parties and media outlets have worked aggressively to undermine ceasefire efforts, reject negotiations, and delegitimize civilian alternatives, framing the war as an existential struggle against "foreign agents" and "enemies of Islam." This rhetoric is not incidental — it is designed to justify indefinite conflict while positioning the Brotherhood as an indispensable wartime ally.
The creation of so-called "popular resistance" structures, endorsed by al-Burhan's command, has provided the Brotherhood's worldview with a new institutional incubator after the formal dissolution of its former ruling party. In effect, the war has allowed the Brotherhood's defenders to re-enter the state through the back door, under the cover of national defense.
A Proven Pattern: From al-Qaeda to the Present
This strategy is not new. The Brotherhood's wartime posture today mirrors its behavior during the 1990s, when Sudan became one of the world's most important hubs for transnational jihadist networks.
Under Brotherhood-dominated governance, Sudan hosted Osama bin Laden from 1991 to 1996, providing him safe haven, business opportunities, and operational freedom. During this period, al-Qaeda established financial, agricultural, and training infrastructure inside Sudan — facilitated by state protection.
The consequences were global. Sudan was later linked to:
- The 1995 attempted assassination of Egypt's president in Ethiopia
- The 1998 bombings of U.S. embassies in Kenya and Tanzania
- The 2000 attack on the USS Cole
These links resulted in Sudan's designation as a state sponsor of terrorism — a designation that would last for nearly three decades.
While the Brotherhood and al-Qaeda differed ideologically – with al-Qaeda preferring armed struggles and the adherents of the Brotherhood preferring gradual infiltration and political power – they converged tactically. Sudan served as a permissive environment where extremist networks could operate with minimal restraint. The lesson is clear: when empowered by the state, the covert Brotherhood has historically enabled forces far more radical than itself.
Hamas, Finance, and the Infrastructure of Militancy
The Brotherhood's relationship with Hamas further illustrates its role as a regional facilitator of militant movements.
Beginning in the early 1990s, Sudan hosted Hamas offices, personnel, and investment vehicles. Brotherhood leader Hassan al-Turabi acted as a political sponsor and mediator, helping Hamas consolidate its regional standing. Over time, Hamas benefited from preferential business treatment, tax exemptions, and unrestricted capital flows through Sudanese companies and charities.
After the fall of Omar al-Bashir in 2019, Sudanese authorities dismantled a network of Hamas-linked companies, seizing real estate, agricultural land, factories, media outlets, and financial firms valued in the tens of millions of dollars. U.S. sanctions later confirmed that Sudanese-based financiers had transferred approximately $20 million to Hamas through these structures.
Sudan was not merely a financial hub — it was a logistical corridor.
Iran: Pragmatic Alliance, Strategic Consequences
Despite Sunni-Shia differences, the Brotherhood's relationship with Iran was driven by strategic pragmatism. Sudan served as a transit point for Iranian weapons destined for Hamas, particularly between 2009 and 2012. Arms originating in Iran and post-Gaddafi Libya moved through Sudan toward Gaza, contributing to Israel's decision to strike Sudanese targets multiple times during that period.
For Iran, Sudan offered geographic reach. For the followers of the Brotherhood, Iranian support provided leverage, resources, and regional relevance. Ideology proved secondary to shared enemies and mutual utility.
The Core of al-Burhan's Regime
Taken together, these patterns lead to an unavoidable conclusion: the Muslim Brotherhood is not an external influence on al-Burhan's regime — it is its ideological and organizational backbone.
The Brotherhood affiliates supply:
- Fighters and militias that reinforce the SAF
- Intelligence and security expertise embedded in state institutions
- Political justification for prolonged war
- Regional networks capable of mobilizing finance, propaganda, and external support
Al-Burhan's leadership, in turn, provides the Brotherhood loyalists with legitimacy, arms, and access to the state — replicating the same bargain that sustained Islamist rule under Omar al-Bashir.
This symbiosis explains why international pressure for negotiations has repeatedly failed. Any meaningful transition to civilian rule would dismantle the Brotherhood's reconstituted power — and that is precisely what the current regime cannot afford.
Why This Matters for the United States
For U.S. policymakers, Sudan's crisis cannot be resolved by focusing solely on personalities or battlefield dynamics. The structural role of the Muslim Brotherhood must be confronted.
A regime such as Sudan's, whose core is built on a movement with a documented history of hosting al-Qaeda, financing Hamas, cooperating with Iran, and undermining democratic transitions, cannot serve as a reliable partner for stability.
Ignoring this reality risks repeating the mistakes of the 1990s — when Sudan was treated as a conventional state actor, even as it incubated networks that would later destabilize the region and threaten U.S. interests.
Sudan's war has many fronts, but its center of gravity remains the same. Until the grip of the Brotherhood's extremists on the state is broken, peace will remain elusive — and instability will remain policy.
Robert Williams is based in the United States.
