Sheltering in a bunker, Iran’s supreme leader names potential successors

Emergency workers at the site of an Iranian missile attack in Haifa, Israel, on Friday, June 20, 2025. Ayatollah Ali Khamenei has not only picked replacements in his chain of military command in case they are killed in Israeli strikes, he has also named three senior clerics to replace him should he, too, be slain. (Daniel Berehulak/The New York Times)

By FARNAZ FASSIHI

Wary of assassination, Iran’s supreme leader mostly speaks with his commanders through a trusted aide now, suspending electronic communications to make it harder to find him, three Iranian officials familiar with his emergency war plans say.

Ensconced in a bunker, the supreme leader, Ayatollah Ali Khamenei, has picked an array of replacements down his chain of military command in case more of his valued lieutenants are killed.

And in a remarkable move, the officials add, Khamenei has even named three senior clerics as candidates to succeed him should he be killed as well — perhaps the most telling illustration of the precarious moment he and his three-decade rule are facing.

Khamenei has taken an extraordinary series of steps to preserve the Islamic Republic ever since Israel launched a series of surprise attacks June 13.

Though only a week old, the Israeli strikes are the biggest military assault on Iran since its war with Iraq in the 1980s, and the effect on the nation’s capital, Tehran, has been particularly fierce. In only a few days, the Israeli attacks have been more intense and have caused more damage in Tehran than Saddam Hussein did in his entire eight-year war against Iran.

Iran appeared to have overcome its initial shock, reorganizing enough to launch daily counterstrikes of its own on Israel, hitting a hospital, the Haifa oil refinery, religious buildings and homes.

But then the United States entered the war as well. President Donald Trump announced late Saturday that the U.S. military had bombed three of Iran’s nuclear sites, including its uranium-enrichment facility deep underground at Fordo, broadening the conflict significantly.

“Our objective was the destruction of Iran’s nuclear enrichment capacity and a stop to the nuclear threat posed by the world’s No. 1 state sponsor of terror,” Trump said in an address to the nation from the White House on Saturday night.

Peering inside Iran’s closely guarded leadership can be difficult, but as of late this past week its chain of command still seemed to be functioning, despite being hit hard, and there were no obvious signs of dissent in the political ranks, according to the officials and to diplomats in Iran.

Khamenei, 86, is aware that either Israel or the United States could try to assassinate him, an end he would view as martyrdom, the officials said. Given the possibility, the ayatollah has made the unusual decision to instruct his nation’s Assembly of Experts, the clerical body responsible for appointing the supreme leader, to choose his successor swiftly from the three names he has provided.

Normally, the process of appointing a new supreme leader could take months, with clerics picking and choosing from their own lists of names. But with the nation now at war, the officials said, the ayatollah wants to ensure a quick, orderly transition and to preserve his legacy.

“The top priority is the preservation of the state,” said Vali Nasr, an Iran expert and professor of international affairs at Johns Hopkins University. “It is all calculative and pragmatic.”

Succession has long been an exceedingly delicate and thorny topic, seldom discussed publicly beyond speculations and rumors in political and religious circles. The supreme leader has enormous powers: He is the commander in chief of Iran’s armed forces as well as the head of the judiciary, the legislature and the executive branch. He is also a Vali Faqih, meaning the most senior guardian of the Shiite faith.

Since the war started, the ayatollah has delivered to the public two recorded video messages, against a backdrop of brown curtains and next to the Iranian flag. “The people of Iran will stand against a forced war,” he said, vowing not to surrender.

In normal times, Khamenei lives and works in a highly secure compound in central Tehran called the “beit rahbari” — or leader’s house — and he seldom leaves the premises, except for special occasions like delivering a sermon. Senior officials and military commanders come to him for weekly meetings, and speeches for the public are staged from the compound.

His retreat to a bunker shows how furiously Tehran has been struck in a war with Israel that Iranian officials say is unfolding on two fronts.

One is being waged from the air, with Israeli airstrikes on military bases, nuclear facilities, critical energy infrastructure, commanders and nuclear scientists in their apartment buildings in residential neighborhoods. Some of Iran’s top commanders were summarily wiped out.

Hundreds of people have also been killed and thousands of others injured, with civilians slain across Iran, human rights groups inside and outside the country say.

But Iranian officials say that they are fighting on a second front as well, with covert Israeli operatives and collaborators scattered on the ground across Iran’s vast terrain, launching drones at critical energy and military structures. The fear of Israeli infiltration among the top ranks of Iran’s security and intelligence apparatus has rattled the Iranian power structure, even Khamenei, officials say.

“It is clear that we had a massive security and intelligence breach; there is no denying this,” said Mahdi Mohammadi, a senior adviser to Iran’s speaker of parliament, Gen. Mohammad Ghalibaf, in a recording analyzing the war. “Our senior commanders were all assassinated within one hour.”

Iran’s “biggest failure was not discovering” the months of planning Israeli operatives had conducted to bring missiles and drone parts into the country to prepare for the attack, he added.

The country’s leadership has been preoccupied with three central concerns, officials say: an assassination attempt against Khamenei; the U.S. entering the war; and more debilitating attacks against Iran’s critical infrastructure, like power plants, oil and gas refineries and dams.

Iran has threatened to retaliate against the United States by attacking American targets in the region, but the options for Iran’s government are complicated, at best. If it retaliates against the American strikes on its nuclear facilities, it could be thrust into a major war with a military superpower.

The fear of assassination and infiltration within Iran’s ranks is so widespread that the Ministry of Intelligence announced a series of security protocols, telling officials to stop using cellphones or any electronic devices to communicate. It has also ordered senior government officials and military commanders to remain below ground, two Iranian officials said.

Almost every day, the Ministry of Intelligence or the Armed Forces issue directives for the public to report suspicious individuals and vehicle movements, and to refrain from taking photographs and videos of attacks on sensitive sites.

The country has also been in a communication blackout with the outside world. The internet has been nearly shut down, and incoming international calls have been blocked. The Ministry of Telecommunications said in a statement that these measures were to find enemy operatives on the ground and to disable their ability to launch attacks.

“The security apparatus has concluded that, in this critical time, the internet is being abused to harm the lives and livelihoods of civilians,” said Ali Ahmadinia, the communications director for President Masoud Pezeshkian. “We are safeguarding the security of our country by shutting down the internet.”

Tehran has largely emptied out after orders by Israel to evacuate several highly populated districts. Videos of the city show highways and desolate streets that are typically clogged with bumper-to-bumper traffic. In interviews, residents of Tehran who remained in the city said security forces had set up checkpoints on every highway, on smaller roads and at entry points in and out of the city to conduct ad hoc searches.

Mohammad Ali Abtahi, a reformist politician and a former vice president, said in a telephone interview from Tehran that Israel had miscalculated Iranians’ reaction to the war. Abtahi said that the deep political factions that are typically in disagreement with one another had rallied behind the supreme leader and focused the country on defending itself from an external threat.

The war has “softened the divisions we had, both among each other and with the general public,” Abtahi said.