In the aftermath of a brutal and unprecedented war between Iran and Israel, Supreme Leader Ayatollah Ali Khamenei, 86, finds himself secluded in a secret bunker somewhere in Iran. Nearly two weeks of incommunicado exile have fueled speculation about his health, safety, and the state of the Islamic Republic. While a US-Qatar brokered ceasefire now holds—albeit tenuously—the war has reshaped Iran’s landscape, weakened its institutions, and deeply shaken its people.
Once considered the unshakable nucleus of Iran’s theocratic system, Khamenei is now widely seen as a diminished figure. The myth of invulnerability, so central to the regime’s narrative, lies in tatters. And even as he prepares for what will likely be a heavily choreographed reappearance on state television, the country he rules over is no longer the one he left behind.
Khamenei’s disappearance during the height of the war speaks volumes about the gravity of the crisis. According to multiple intelligence leaks, Israel had placed the supreme leader on a high-value target list, prompting emergency action by the Iranian security apparatus. Reports indicate that even the country’s top officials were left in the dark, raising alarm over the vacuum of authority at a critical moment.
Despite US President Donald Trump’s private assurances to Israel not to target Khamenei, Israeli Prime Minister Benjamin Netanyahu has refused to confirm any such restriction. The war’s asymmetry—marked by Israeli air superiority, precision strikes, and rapid decapitation of Iran’s military leadership—has left Tehran’s command structure fractured.
Khamenei’s long silence, likely intended as a strategic retreat, has instead underscored his vulnerability. For a regime built around the image of divine authority and steadfast resistance, that silence may prove devastating.
From the first day of hostilities, Iran’s defenses were overwhelmed. Israeli jets, drones, and long-range missiles swiftly disabled airbases, anti-aircraft systems, and command centers. The Revolutionary Guard Corps (IRGC), long the backbone of Iran’s military and ideological enforcement, suffered massive losses. Key commanders were killed in targeted strikes, with intelligence suggesting that Israeli forces had detailed operational maps of Iran’s most sensitive sites.
Military analysts estimate that Iran lost at least 40% of its aerial and missile defense capabilities. The cost of these attacks was not just in hardware but in morale. For a nation that had long claimed regional deterrence based on its ballistic missile arsenal and proxy network, the revelation of how quickly its core was breached has stunned observers.
Even Iran’s nuclear program, the crown jewel of its strategic deterrence, was hit. Though details remain murky, satellite imagery and insider accounts point to heavy bomb damage at Fordow, Natanz, and Arak. While Iran has claimed to have moved its stockpile of 60% enriched uranium to an undisclosed location, the full operational integrity of its enrichment infrastructure is now in question.
“What was it all for?” is a question now echoing through the streets of Tehran and whispered in the corridors of Qom.
Since ascending to the role of Supreme Leader in 1989, Khamenei has entrenched Iran in an ideological mission: exporting revolution, resisting Western hegemony, and destroying the state of Israel. Yet, after four decades, that mission has left Iran internationally isolated, economically crippled, and domestically exhausted.
International sanctions imposed over Iran’s nuclear ambitions had already strangled its economy. Once the world’s fourth-largest oil exporter, Iran now struggles to meet even basic import needs. The war has only worsened this reality. Infrastructure in cities like Isfahan, Mashhad, and Shiraz has been damaged or destroyed. Key oil facilities in Khuzestan were hit, and the Strait of Hormuz, long Iran’s ace card, saw major disruptions.
“Ali Khamenei is likely to become the Islamic Republic’s last ‘Supreme Leader’ in the full sense of the word,” says Professor Lina Khatib, a visiting scholar at Harvard University. “The war has delegitimized the ideology he stood for.”
Khamenei’s belief that nuclear weapons would ensure Iran’s immunity from foreign attack now looks tragically flawed. Not only did Israel strike regardless, but it did so decisively and, for now, with impunity.
As bombs rained down, discontent surfaced. Reports from within Iran indicate that some high-ranking former regime officials attempted to reach out to Qom’s more moderate clerics, suggesting a possible intervention to replace Khamenei. While no formal move materialized, the mere existence of such talks signals the deepening fracture within the regime’s elite.
“There will be a reckoning,” warns Professor Ali Ansari of the University of St Andrews. “The leadership is deeply divided, and the public has lost patience.”
This growing disillusionment is not new. Over the years, waves of protests—from the 2009 Green Movement to the 2022 women-led uprising—have signaled mounting frustration. But the war has accelerated this unrest. A shattered economy, combined with national humiliation, is a volatile mix.
For now, dissent remains suppressed. The IRGC, even weakened, still commands vast domestic power. Over the last two weeks, at least six individuals have been executed on charges of spying for Israel. Around 700 others are in custody. Activists fear a broader crackdown is imminent.
“If the regime is unable to supply basic goods and services, then there will be growing anger and frustration,” says Professor Ansari. “But it won’t explode immediately. It will simmer. It’s a slow burn.”
Ironically, amidst the devastation, many Iranians found solidarity. Accounts have emerged of townspeople welcoming refugees from bombed cities, shopkeepers giving away food, and communities banding together. But this unity was not in support of the regime. Rather, it was an instinctive act of survival and mutual care.
“There was a clear distinction in people’s minds,” says a Tehran-based sociologist. “Defending the homeland did not mean defending the regime.”
Still, the idea of regime change remains deeply complicated. While many Iranians privately hope for a new system, they remain wary of foreign-engineered transitions. The scars of the 1953 CIA-backed coup, and more recently, the chaos in post-war Iraq, loom large.
“No one wants a vacuum,” says a former Iranian diplomat now in exile. “The regime has ensured that no viable opposition exists. If it collapses suddenly, chaos will follow.”
Khamenei’s strategy of quashing all dissent—jailing political rivals, silencing media, and forcing reformist leaders into exile—has worked too well. Outside Iran, opposition groups remain fractured. The once-prominent Mujahedin-e-Khalq (MEK) has little credibility at home. Monarchists are divided. Secular reformists lack coordination.
During the war, when many believed the regime’s collapse was imminent, there was no alternative ready to step in.
“It’s a tragic paradox,” says Professor Khatib. “The system is brittle and unpopular, but there’s nothing cohesive to replace it with.”
The most likely scenario in the event of leadership vacuum is either a military takeover by IRGC hardliners or a transition to a council-style leadership. Neither promises a democratic future.
Few in Iran believe the ceasefire will hold. Israel, having demonstrated overwhelming air superiority, is reportedly waiting for strategic opportunities to strike again. With much of Iran’s defenses crippled, Tel Aviv may yet return to destroy what remains of Iran’s nuclear capabilities.
The Israeli Defense Forces (IDF) Chief of Staff Eyal Zamir stated that Iran began the war with about 2,500 surface-to-surface missiles. Though Iran managed to launch devastating barrages, an estimated 1,500 missiles remain. These are likely hidden in tunnels under the Zagros Mountains—strategic bunkers designed to withstand airstrikes.
Their existence is a ticking time bomb, both for Israel and the region.
Meanwhile, the possibility of Iran exiting the Nuclear Non-Proliferation Treaty (NPT) looms. The Iranian parliament has voted to reduce cooperation with the IAEA. If the vote passes through the Guardian Council and receives Khamenei’s assent, Iran could be on the brink of a formal nuclear breakout.
Experts warn that Iran’s 60% enriched uranium stockpile, if further enriched to weapons-grade, could yield nine nuclear bombs. Before the war, a new secret enrichment facility was reportedly near completion.
At 86, ailing and under siege, Khamenei knows the clock is ticking. Insiders suggest he is weighing succession plans. One possibility is the elevation of his son, Mojtaba Khamenei—already a powerful cleric and IRGC ally. Another is the formation of a ruling council composed of hardline clerics and Guard commanders.
Either outcome would likely preserve the ideological core of the regime, albeit with adjustments. Yet many observers believe the Islamic Republic, as conceived in 1979, may not survive Khamenei’s departure.
“The era of absolute clerical rule may be over,” says Professor Ansari. “The next phase could be a hybrid of military-theocratic governance—more authoritarian, less ideological.”
As Ayatollah Khamenei prepares to emerge from his hidden sanctuary, he faces a broken country, a fractured regime, and a disillusioned population. Victory claims on state television may be met with hollow stares. The war with Israel has exposed Iran’s vulnerabilities—military, ideological, and institutional.
What comes next is uncertain. Will the regime double down on repression, or open a path to reform? Will Israel strike again? Will the nuclear issue reignite a wider conflict?
