Inside the plan to kill Ali Khamenei

Not all of the details of the latest operation are known. Some may never be made public, in order to protect sources and methods still being used to track down other targets.

But killing Khamenei was a political decision, not simply a technological achievement, said more than half a dozen current and former Israeli intelligence officials interviewed for this story.

When the CIA and Israel determined that Khamenei would be holding a meeting on Saturday morning at his offices near Pasteur Street, the chance to kill him alongside so much of Iran’s senior leadership was especially opportune.

They assessed that hunting them down after a war had properly begun would have been much harder, since the Iranians would quickly embark on evasive practices, including heading underground to bunkers immune to Israeli bombs.

Khamenei, unlike his ally Hezbollah leader Hassan Nasrallah, did not live in hiding. Nasrallah had spent years of his life in underground bunkers, dodging several Israeli assassination attempts until September 2024, when Israeli fighter jets dropped as many as 80 bombs over his hideout in Beirut, killing him.

Instead, Khamenei had mused in public about the possibility of being killed, dismissing his own life as inconsequential to the fate of the Islamic Republic – in fact, some Iran experts said he expected to be martyred.

But during wartime, said one of the people interviewed, he did take some precautions. “It was unusual for him to not be in his bunker – he had two bunkers – and if he had been, Israel wouldn’t have been able to reach him with the bombs that they have,” the person said.

Even in June 2025, in the throes of a full-blown war, Israel made no known attempts to bomb Khamenei. It had instead targeted mostly the leadership of the Islamic Revolutionary Guards Corps, missile launchers and stockpiles and Iran’s nuclear facilities and scientists.

While Donald Trump had repeatedly threatened to attack Iran in recent weeks, building up an “armada” off its shores, negotiations between the US and Iran over the Islamic Republic’s nuclear programme were meant to continue this week.

The mediator Oman said Iran was willing to make concessions that might help stave off a war and described the most recent meeting last Thursday as fruitful.

In public, the US president grumbled that things were moving too slowly. But a person familiar with the matter said that, in private, Trump was “dissatisfied with the Iranian responses”, paving the way for war.

A person briefed on the situation said the attack on Iran had been planned for months, but officials adjusted their operation after the US and Israeli intelligence confirmed that Khamenei and his senior officials would be meeting in his compound in Tehran on Saturday morning.