Iran Supreme Leader Ali Khamenei runs ‘state within state’ shadow apparatus

FIRST ON FOX: A new report detailing the inner workings of Ayatollah Ali Khamenei’s office says the Islamic Republic’s real command structure lies not in Iran’s visible government, but in a shadow apparatus designed to preserve regime control even if the supreme leader himself disappears from public view.

The report, Unmasking the Bayt: Inside the Supreme Leader’s Office, published by United Against Nuclear Iran (UANI) and authored by Saeid Golkar and Kasra Aarabi, describes the Bayt, the Office of the Supreme Leader, as a vast institutional network embedded across Iran’s military, economy, religious institutions and state bureaucracy.

“It is the hidden nerve center of the regime in Iran… it operates as a state within a state,” Aarabi said in an interview with Fox News Digital.

According to Aarabi, the system allows Khamenei to oversee and influence decision-making at every level of the Islamic Republic, including nuclear policy, war planning and internal security.

“This is what gives Khamenei absolute control. It’s not the visible state, this is the invisible state,” he said.

The report estimates roughly 4,000 people operate inside the Bayt’s core structure, with tens of thousands more working through affiliated institutions across the country.

“There’s around 4,000 close employees… think of them as commissars… the real policymakers,” Aarabi said. “Beyond that, the Bayt’s umbrella has 40,000 individuals working for it… entrenched at every single layer of policy, every single state entity.”

The report maps a tightly controlled inner circle at the top of the Bayt, including Khamenei’s sons, particularly Mojtaba Khamenei, who is described as operating like a “mini-supreme leader” within his father’s office. 

It details how the structure reaches directly into Iran’s military chain of command, with senior promotions requiring approval from the Supreme Leader’s office and parallel counterintelligence bodies monitoring loyalty across the armed forces. The Bayt, the report says, also plays a decisive role in nuclear negotiations and wartime decision-making, ensuring ultimate authority remains concentrated around the supreme leader.

The network, Aarabi said, effectively duplicates state ministries inside Khamenei’s office, allowing direct oversight and ideological enforcement across government agencies, universities and cultural institutions.

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The report also outlines how the Bayt sustains regime durability through control of the economy, religious institutions and the education system. Networks of foundations and conglomerates tied to the supreme leader oversee major sectors of Iran’s economy, while clerical institutions, universities and cultural bodies are monitored by embedded representatives tasked with enforcing ideological compliance and suppressing dissent.

“Think of the Bayt as the nucleus of the core power of the regime,” Aarabi said.

The findings come amid renewed speculation about Khamenei’s health and reduced public visibility, as well as growing regional tensions and the possibility of military confrontation involving Iran.

Aarabi pushed back on suggestions that Khamenei’s absence from public appearances signals weakening authority or internal fragmentation.

“We saw this during the 12-day war… even if he is hiding in a bunker, he is in full control. The Bayt has been tightening Khamenei’s grip on power,” he said.

The structure, he argued, was deliberately built to function even without the supreme leader physically present.

“Even if he is eliminated, the Bayt as an institution enables the supreme leader to function,” Aarabi said. “Think of the supreme leader as an institution rather than just a single individual.”

The report places the Bayt at the top of Iran’s power hierarchy, above the Islamic Revolutionary Guard Corps and the formal government.

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“The Bayt is the core apparatus… the strategic policymaking body that is driving the ballistic missile program, the nuclear program, [and] regional destabilization,” Aarabi said.

The implications, he added, are significant for policymakers in Washington and across the region, particularly as the U.S. weighs options for confronting Iran’s nuclear program and regional activities.

“Eliminating Khamenei in isolation on its own is not enough… you have to dismantle this extensive apparatus that he has created,” Aarabi said.

Instead, any effort to weaken the regime would require targeting the broader institutional structure surrounding the supreme leader, not just the individual at its center.

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“It involves a comprehensive strategy… cyber operations, sanctions, [and] a military component,” he said. “For any meaningful change in Iran… you have to go after the core nucleus of power within the Islamic regime, and that is the Bayt.”

He said on reports of Khamenei being a target that, “the elimination of Khamenei alone is not enough… dismantling the extensive apparatus of the Bayt is essential,” he added.

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