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The assassination of Iran’s supreme leader, Ayatollah Ali Khamenei, was the culmination of decades of painstaking intelligence gathering by Israeli secret services, with crucial technological resources and manpower provided over the last six months by the CIA and other US intelligence services, which culminated in a single concentrated burst of lethal violence to decapitate the Iranian regime, according to experts, veteran spies and officials in Israel and the US.
Khamenei was killed along with seven “members of the top Iranian security leadership who had gathered at several locations in Tehran” and about a dozen members of his family and close entourage in near-simultaneous strikes within 60 seconds, military officials in Israel said. Forty other senior Iranian leaders also died in the attack.
The killing of Khamenei, 86, opened the air offensive launched this weekend by Israel and the US in an effort to overthrow the radical clerical regime in Tehran, plunging the Middle East into renewed chaos and violence.
Some experts and intelligence veterans, however, described a possible strategic error that could alienate potential supporters or open the way for more radical opponents in the future.
“The problem is that Israel is in love with assassinations … and we never learn that it is not the solution. We have killed all the leaders of Hamas. They are still there. It’s the same with Hezbollah. The leaders are always replaced,” said Yossi Melman, a respected Israeli analyst and author specialising in intelligence.
Israel has a long history of conducting assassinations overseas, but has never before killed a head of state.
Amos Yadlin, a former head of Israel’s military intelligence service, said the strike was “a tactical surprise, an operational surprise” because the general expectation was that Israel would attack in darkness, replicating the surprise strike which opened the 12-day war in June.
The timing of the assassination was determined by information the CIA gleaned about a meeting of top Iranian officials at a leadership compound in the heart of Tehran scheduled for Saturday morning. Most critically, the CIA was able to tell Israeli counterparts that Khamenei would be at the site and the timing of the meeting, according to the New York Times.
Israeli spies had also been tracking Khamenei for many years, building a minutely detailed file on his daily routine and those of his family members, associates, allies and those charged with keeping him safe.
“It’s like a giant jigsaw puzzle. You are putting all these scraps of information together. Where you don’t have [reliable data] you look further into those. It will be everything: how do they get food, what happens to their trash … We all get up and go to bed, we all eat and drink,” said a former CIA veteran with decades of experience in tracking high-profile terrorist targets.
“We are in a world where information and data is so multi-layered that there is no one who doesn’t leave some kind of trail. Everything you do leaves a print.”
Reuel Gerecht, a former CIA targeting officer who worked on Iran and an analyst at the Foundation for the Defense of Democracies, said the US would have been able to bring significant technological assets into play, though it was Israel that had built the networks of agents on the ground capable of supplying human intelligence and carrying out covert operations within Iran.
Gerecht said reports in the Israeli media that a photograph of Khamenei’s remains were shown to Donald Trump and Israel’s prime minister, Benjamin Netanyahu, were plausible.
“The technological capacity of the US is extremely impressive and the tech does matter a lot, but I don’t think that the [CIA] had a lot to bring to the table in terms of [human intelligence] or covert action networks,” he said.
“If you combine the technological capacity with the networks on the ground that would certainly amplify its effectiveness.”
The Mossad, an abbreviation of the Institute for Intelligence and Special Operations in Hebrew, has been focused on Iran for decades, and has built deep networks of informants, agents and logistics there. This has allowed a series of operations including the assassination with a remote-controlled automatic machine gun of a top Iranian nuclear scientist travelling at speed in a car on a remote road, the infection with malware of computers running key parts of Iran’s nuclear programme and the theft of an archive of nuclear documents. The political leader of Hamas, Ismail Haniyeh, was assassinated in 2024 with a bomb placed in his favourite room in a government guesthouse in Tehran.
During the 12-day war in June, Israeli agents managed to identify the homes of Iranian nuclear scientists, intelligence officials and military commanders – information that allowed dozens to be killed in a first wave of surprise attacks.
Melman said the Mossad had made a key change of strategy almost 20 years ago, deciding to recruit local agents within Iran who were given state-of-the-art equipment and high levels of training.
David Barnea, who has led the Mossad since 2021, built a special department for a “foreign legion” of agents who have been deployed across the Middle East on sensitive missions.
Such agents were easier to recruit in Iran, where many people were opposed to the ruling regime, than elsewhere, Melman said.
Israel was poised to assassinate Khamenei last year, but Trump was reluctant to risk regional escalation and the reaction of allies concerned by the killing of a head of state. Such reservations appear to have disappeared in the months since the brief conflict last year, which ended shortly after US bombers attacked Iranian nuclear facilities.
Israeli military officials said there had since been “really very enhanced cooperation” between Israel and the US on Iran.
The flow of information from the Mossad’s networks on the ground in Iran would have been merged last week with intelligence gathered through communications intercepted by the US.
“I wouldn’t be surprised if they locked on to a variety of means to track [Khamenei],” said Gerecht. “The Iranians are pretty sloppy. They love their phones. So maybe the supreme leader had a stack of burner phones but it’s about people he was calling regularly.”
Finally, information would have been fed through to the US and Israeli militaries to allow precise targeting information to be compiled and the orders to be given for that brief but deadly and destructive minute.
“Sixty seconds. That’s all it took for this operation, but it is the product of years in the making,” said Oded Ailam, a former head of the Mossad’s counter-terrorism division and a researcher at the Jerusalem Center for Security and Foreign Affairs. “The modern battlefield is no longer defined only by tanks and aircraft. It is defined by data, access, trust and timing. One minute can change a region.”
The CIA veteran said they believed the assassination was a mistake: “I think it was the wrong thing to do. Not from an ethical perspective - I have been fine with killing people, a lot of them in fact - but from a long-term strategic perspective.
“I know that when you take out someone’s leader you don’t solve the problem. You just create a new one.”
