Israel's secret intelligence operations in Iran: Hacked phones, deep-cover agents and covert warehouses

Irish Times

6 hours ago

Last year, an
Israeli
telecoms executive working in Europe had a call from an old friend back in Tel Aviv: could he help design a phone that looked like a cheap Android but could transmit encrypted data that mimicked social media traffic?
Around the same time, a reservist working at an Israeli health start-up got a call from Unit 9900, a tiny part of the Israeli military that seeks clues in vast data sets. Could he tweak an algorithm he had worked on during his military service, so a dedicated server could sift through satellite images of fuel trucks and separate those carrying petrol from those with missile propellant?
Neither was told exactly how their efforts shaped last week's opening salvo in
Israel's aerial assault on Iran
, which stunned the country with both its depth and precision. More than a dozen security chiefs and nuclear scientists were assassinated nearly simultaneously; entire aerial defence arrays were destroyed before they could fire off a single interception; and a large number of missile launch sites were identified and destroyed.
How Israel's security services pulled off parallel operations combining the work of its military intelligence arm Aman, with the foreign spy service Mossad into such an effective assault may never fully become public. But early hints are trickling out – some from authorised leaks aiming to embarrass Iran, others from people familiar with the operations speaking to the Financial Times on the condition of anonymity.
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They describe a sprawling, multiyear operation that leant on every possible asset from which Israeli intelligence could draw – commercial satellites, hacked phones, deep-cover agents recruited locally, covert warehouses to assemble drones and even miniaturised weapons systems fitted into everyday vehicles.
The goal, the people said, was to create a densely populated bank of targets to take out in the first hours of a military operation. One called it the Israeli version of 'shock and awe'; another said it aimed to embrace the 'audacious'.
A former Israeli official described the project as the result of 'millions of dollars and years of efforts' to address what Israel considers an existential threat. 'When you work for so many years, investing everything you have – human intelligence, open source intelligence, money – you eventually get an outcome' like this, they said.
In the run-up to the assault, Aman identified so-called centres of gravity to focus on, such as firepower hubs and the nuclear programme. It cross-referenced thousands of intelligence sources, and by March of this year, had started to populate the target bank.
In a clue as to how these targets may have been tracked, a technical team in the military was consulted last October about how it had monitored
Hassan Nasrallah
, leader of the Iran-backed Lebanese militant group
Hizbullah
, who Israel had killed days earlier. Their sophisticated, nearly automated system had produced with near certainty his location once every 24 hours.
An Israeli air strike on Tehran, Iran. Photograph: Arash Khamooshi/ New York Times
The aftermath of an Israeli air strike on Tehran, Iran. Photograph: Arash Khamooshi/ New York Times
Israel's assault on Iran has yet to achieve its grand strategic goal – the destruction of the Islamic republic's nuclear and ballistic missile programmes – or its additional aim of weakening the regime to the point of collapse. But its first hours last week underlined the ambitious and comprehensive list of targets that Israeli intelligence operatives keep constantly updated.
The opening shots of the campaign focused on at least four types of targets within a few minutes: military officials high in the chain of command; aerial defences around the most strategic sites; parts of two major nuclear installations; and missile launch sites in western Iran that had been identified as immediate response threats. In this way, Israel could take advantage of the surprise factor.
'The initial attack, the opening strike, was the beginning of the campaign. We're not done yet,' said Miri Eisin, a former senior intelligence officer. 'To be able to target 15 different people at the same time – now that's not easy – and since you've taken out the decision makers, you're delaying their response to buy more time.'
The Israeli success has sowed at least some panic within Iran's security establishment, which has been repeatedly embarrassed in the past by Mossad. The spy agency's headquarters on the northern outskirts of Tel Aviv has been a repeated target of Iranian ballistic missiles.
A former senior commander in Iran's elite Revolutionary Guards this week urged people to check their roofs for micro drones, claiming Iranian opposition groups had been paid to smuggle them into major cities. Police chief Ahmad-Reza Radan urged spies for Israel to turn themselves in to receive 'Islamic clemency'.
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Fars News Agency, affiliated with the Revolutionary Guards, reported warnings that mobile phones were being used not just for surveillance but also for assassination.
'The most important decision must be this: all mobile phones belonging to commanders, senior officials, nuclear scientists – and even their families – should be put aside,' said hardline MP Hamid Rasaee.
An oil storage facility on fire after Israeli air strikes on Tehran, Iran. Photograph: Arash Khamooshi/New York Times
But such measures would be unlikely to make a difference at this point, said people familiar with Israel's operations inside Iran. The telecoms executive declined to discuss whether his software was eventually deployed in Iran, but bragged that many hundreds of people were often using it simultaneously around the world.
Israel is now hunting the remnants of Iran's aerial defences and has nearly complete aerial superiority. It lost what appeared to be a Hermes 900 surveillance drone to an Iranian missile but has had no other publicly acknowledged losses of military hardware. Its air force has been left free to attack anywhere in Iran at will.
Iranian intelligence operations inside Israel pale in comparison. A handful of Israeli citizens have been arrested and prosecuted for collecting information for Iran, while Iranian hackers appear to have broken into the mobile phone of a family member of David Barnea, the Mossad chief, in recent years, with Iran publicly taking credit for the breach.
Its counter-intelligence teams have arrested several people and accused them of working for Israel, and recently executed one. But not a single Israeli is known to have been captured, hinting at a large-scale recruitment of local operatives – either unwittingly or for cash – or people opposed to the regime in Tehran.
In comparison, Mossad has repeatedly carried out daring assassinations of Iranian nuclear scientists, including one in 2020 apparently carried out by a remotely operated machine gun mounted on a truck that self-destructed.
Iranian media reported that thousands had fled Tehran as Iran and Israel launched new waves of missile strikes at each other. Video: Reuters
It has spirited away thousands of documents from Iran's nuclear archive for prime minister
Binyamin Netanyahu
to show off on live television and assassinated a senior
Hamas
leader in an Iranian government guest house last year as he visited for president Masoud Pezeshkian's inauguration.
Adding to its mystique, for the first time in its history, Mossad released footage it said showed its commandos working inside Iran, launching attack drones and guided missiles that took out Iranian air defences and missiles.
'From an intelligence perspective, [the entire campaign] is as impressive a feat as we've seen in modern warfare – complete intelligence domination and penetration, on an unprecedented scale in recent memory,' said a former US defence official.
'I can't think of a conflict where one party so thoroughly understood the contingency plans of its enemy and the movement of its leadership.'
Israel's success against Hizbullah, in a similar surprise campaign last year, and now in the early days of full-scale conflict with Iran, contrasts with its failure to predict or prevent the October 7th, 2023, cross-border attack by Hamas, the Palestinian militant group it had clearly underestimated.
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Its latest achievements showed the capabilities of Israeli intelligence and military units when they were directed and well-resourced, said Eisin.
'The Islamic regime of Iran has been the top priority of Netanyahu and the entire security community. You are investing your capabilities of your entire security and intelligence community in finding out this information and then acting upon it.'
But, she added: 'That makes me worry about the hubris that comes with this kind of success.' – Copyright the Financial Times Limited 2025
'A war that's been planned for a decade' - why Israel has attacked Iran and what happens next
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