Israel’s attacks leave Iran’s supreme leader exposed—with no good options

Tehran fired dozens of ballistic missiles at Tel Aviv Friday after Israeli warplanes carried out waves of strikes across Iran a day earlier, targeting the country’s nuclear facilities and killing several of its highest-ranking commanders and senior scientists.

Israel’s attacks amounted to the most serious blow struck in a confrontation that erupted between the two longtime foes on Oct. 7, 2023. Iran has so far been unable to respond in kind. Most of the missiles it fired at Tel Aviv were intercepted or caused little damage.

Now, Khamenei faces stark choices—and no good options. Iran’s bruising fight with Israel has left its military weakened. Further retaliation risks being insufficient to deter future attacks and prompting Israel to hit back harder.

Attacks on shipping in the Red Sea or other U.S. interests or personnel will likely draw an American response, something Khamenei has historically tried to avoid. Yielding to pressure and striking a nuclear deal with the U.S. that severely curbs Iran’s enrichment capability will be seen among Khamenei’s hard-line supporters, whom he has increasingly come to rely on, as an unacceptable capitulation.

For decades, Khamenei was the architect behind Iran’s military and political expansion in the Middle East, using the Revolutionary Guard and its network of allied Shiite militias. He secured his rule at home by building fierce loyalty among those who supported him, and a pervasive surveillance state to suppress those who didn’t.

Now, the octogenarian ruler who has led Iran since 1989 will likely spend the autumn of his life fighting—not to expand, but to salvage the Islamic Republic he helped build into a regional powerhouse.

“If he is honest with himself, he will admit that he has lost. Everything he has worked for is crumbling before his eyes," said Afshon Ostovar, associate professor at the Naval Postgraduate School in Monterey, Calif. “The ship that he stewarded has run aground."

Khamenei has flaunted Iran’s military might, but until recently, it remained untested. That changed with the attack by Hamas—an Iranian ally—on Israel on Oct. 7, 2023.

Since then, while waging war in Gaza, Israel has killed nearly a dozen senior Iranian military commanders, including, on Friday, the head of the Revolutionary Guard, the armed forces chief of staff and the commander who oversaw its ballistic missile program. Israel also crippled Iran’s chief regional allies, Hamas and Hezbollah, while a third, Syrian President Bashar al-Assad, was toppled in December.

Iranian Major Gen. Hossein Salami, commander of Iran’s Islamic Revolutionary Guard Corps, was killed in Israel’s attack on the Islamic Republic.

After building up a military presence in the region, including heavily armed militia fighters on the border with Israel, Khamenei and his senior advisers gravely underestimated Israel’s willingness to confront it with force, said Hamidreza Azizi, visiting fellow at the German Institute for International and Security Affairs, or SWP.

Even as tensions rose so high that the U.S. earlier this week withdrew diplomatic personnel from Iraq, the top echelon of Iran’s security establishment were apparently not placed in secure facilities.

“Most of them were targeted in their homes. It shows a level of overconfidence that is not comprehensible, really, in a situation like this," Azizi said.

The way Israel has been able to penetrate Iranian intelligence and seemingly target its top officials at will is a problem for the supreme leader. Firstly, it makes Khamenei himself vulnerable to being targeted.

“If Netanyahu’s goal actually is to eradicate the part of the nuclear program that can be weaponized, and to topple the regime, that will require a lot more," said Rasmus Christian Elling, associate professor of Iranian studies at the University of Copenhagen. “And perhaps that’s what we’re going to see in the coming weeks," he said.

Secondly, Khamenei’s rule partly depends on being a guarantor of national security. For all its unpopularity at home, the Islamic Republic has for decades provided relative safety for its citizens from the wars and terrorist attacks that ravaged neighboring countries.

Since Khamenei came to power shortly after an eight-year war with Iraq, one of the worst global wars of the past century, Iran has kept hostile forces away from its soil. Over the past decade, while Islamic State killed tens of thousands in neighboring Iraq and Afghanistan, the extremist group carried out four major attacks in Iran that killed roughly 150 people—fewer than it killed over the same period in France.

The security structure that is now crumbling around Khamenei has been in place since the early days of the Islamic Republic. The revolutionaries behind the 1979 ouster of the American-backed shah vowed to protect their new theocratic state from the kind of uprising that they had just pulled off. To that end, they established the Islamic Revolutionary Guard Corps and a pervasive intelligence service. Israel has exposed both as increasingly fragile.

Between 2010 and 2012, Tehran accused Israel of killing four nuclear scientists inside Iran. In 2020, Mohsen Fakhrizadeh, regarded as the father of Iran’s nuclear weapons program in the 1990s and 2000s, was killed by a remote-controlled machine gun in an audacious, suspected Israeli attack.

Since Oct. 7, 2023, Israel has killed several top Iranian commanders in Syria. It blew up Hamas’ political leader Ismail Haniyeh in a guesthouse in Tehran by placing a bomb in his room. And on Friday, it targeted several of Iran’s most prominent commanders simultaneously.

Part of the attack on air-defense systems and missile launchers was carried out with explosive drones and other guided weapons, smuggled into Iran by agents from Israel’s spy agency Mossad, according to an Israeli security official.

Still, Iranians are unlikely to seize the moment to foment an uprising, largely because their leaders will do what it takes to protect their rule, said Ostovar.

“Even though Iran has lost its ability to wage a serious war against its adversaries, it can still wage a serious war against its citizens," he said. “I think it’s actually a very dangerous time for people in Iran."

Iran is in a much weaker position beyond its borders. Its longtime tool of deterrence—its regional militias—have been decimated. Its two missile attacks against Israel over the past year were largely unsuccessful.

Yet, Khamenei hard-line supporters, who he relies on, will demand a defiant response to what they see as a continuing Israeli campaign, said Azizi, of SWP. They are unlikely to favor an immediate continuation of nuclear negotiations with the U.S., which were scheduled to resume for a sixth round on Sunday.

“It’s a choice between continuing this war, engaging full-force, or surrender," he said. “It’s already clear to people within the system that regardless of whether and how they respond, Israel is going to continue."

Write to Sune Engel Rasmussen at sune.rasmussen@wsj.com