ProPublica is a nonprofit newsroom that investigates abuses of power. Sign up to receive our biggest stories as soon as they’re published.
Reporting Highlights
Covert Ops: Commandos that the Mossad, Israel’s intelligence service, recruited from Iran and neighboring nations destroyed Iranian air defenses in the first hours of a June attack.
Intelligence Gathering: Israeli operatives identified the bedrooms in which Iranian nuclear scientists were sleeping, enabling precise airstrikes.
Cyber Deception: Israel sent a fake message that summoned senior Iranian military leaders to a phantom meeting in a bunker that was then bombed by Israeli jets.
These highlights were written by the reporters and editors who worked on this story.
In the early morning hours of June 13, a commando team led by a young Iranian, S.T., settled into position on the outskirts of Tehran. The target was an anti-aircraft battery, part of the umbrella of radars and missiles set up to protect the capital and its military installations from aerial attack.
Across the country, teams of Israeli-trained commandos recruited from Iran and neighboring nations were preparing to attack Iranian defenses from within.
As described by their handlers, their motives were a mix of personal and political. Some were seeking revenge against a repressive, clerical regime that had imposed strict limits on political expression and daily life. Others were enticed by cash, the promise of medical care for family members or opportunities to attend college overseas.
The attack had been planned for more than a year by the Mossad, the Israeli intelligence service. Just nine months earlier, the spy agency had shocked the world with its technical prowess — executing a plot hatched in 2014 by its director at the time, Tamir Pardo, that crippled Hezbollah by detonating pagers booby-trapped with tiny but lethal amounts of explosives. According to Hezbollah, the blasts killed 30 fighters and 12 civilians, including two children, and injured more than 3,500.
At 3 a.m. on June 13, S.T. and a foreign legion of roughly 70 commandos opened fire with drones and missiles on a carefully chosen list of anti-aircraft batteries and ballistic missile launchers. (His handlers in the Mossad would only tell us his initials.) The next day, another group of Iranians and others recruited from the region launched a second wave of attacks inside Iran.
In detailed interviews, 10 present and former Israeli intelligence officials described the commando raids and a wealth of previously undisclosed details of the country’s decadeslong covert effort to prevent Iran from building a nuclear bomb. They requested anonymity so they could speak freely.
The officials said the commando attacks were pivotal in June’s airstrikes, allowing Israel’s air force to carry out wave after wave of bombing runs without losing a single plane. Informed by intelligence gathered by the Mossad’s agents on the ground, Israeli warplanes pounded nuclear facilities, destroyed around half of Iran’s 3,000 ballistic missiles and 80% of its launchers, and fired missiles at the bedrooms of Iranian nuclear scientists and military commanders.
As they had with the pagers, Israeli spies took advantage of their ability to penetrate their adversary’s communications systems. Early in the aerial attack, Israeli cyberwarriors sent a fake message to Iran’s top military leaders, luring them to a phantom meeting in an underground bunker that was then demolished in a precision strike. Twenty were killed, including three chiefs of staff.
The strategic map of the region has been dramatically redrawn since the Oct. 7, 2023, attacks in which Hamas killed more than 1,200 Israelis and took 251 hostages. Public attention, particularly in recent weeks, has focused on Israel’s retaliation against Gaza, which has caused scores of thousands of deaths and a deepening famine that has been globally condemned.
The secret war between Israel and Iran has attracted far less public attention but has also played a significant role in the region’s changing balance of power.
In 2018, Israeli-trained operatives broke into an unguarded Tehran warehouse and used high-temperature plasma cutters to crack safes containing drawings, data, computer disks and planning books. The material, weighing over 1,000 pounds, was loaded onto two trucks and driven into neighboring Azerbaijan. Israeli Prime Minister Benjamin Netanyahu displayed the material at a press conference in Tel Aviv and said it proved Iran had been lying about its nuclear intentions.
Two years later, the Mossad killed one of Iran’s top physicists, using artificial intelligence-enhanced facial recognition to direct a remotely operated machine gun parked on a roadside near his weekend house.
In the lead-up to June’s air attacks, according to Israeli planners, they arranged for unwitting truck drivers to smuggle into Iran tons of “metallic equipment” — the parts for the weapons used by the commando teams.
Israeli officials said these operations reflect a fundamental shift in the Mossad’s approach that began about 15 years ago. The agents in Iran who broke into the safes, set up the machine guns, blasted the air defenses and watched the scientists’ apartments were not Israelis. All were either Iranians or citizens of third countries, according to senior Israeli officials with direct knowledge of the operations. For years, such missions in Iran had been the exclusive work of Israeli field operatives. But officials said the growing unpopularity of the Iranian regime has made it much easier to attract agents.
S.T. was one of them. Israeli officials said he grew up in a working-class family in a small town near Tehran. He enrolled in college and was living a seemingly ordinary student life, when he and several classmates were arrested by Iran’s feared Basij militia and taken to a detention center where they were tortured with electric shocks and brutally beaten.
S.T. and his friends were ultimately released, but the experience left him enraged and eager for revenge. Soon after, a relative living overseas provided his name to an Israeli spy whose job was to identify disaffected Iranians. Messages were exchanged via an encrypted phone app, and S.T. accepted a free trip to a neighboring country.
A case officer from the Mossad invited him to work as a covert operative against Iran. He agreed, asking only that Israel pledge to take care of his family if anything went wrong. (Iran summarily executes anyone caught spying for foreign countries, especially Israel.)
He was trained for months outside of Iran by Israeli weapons specialists. Just before the attack was to begin, he and his small team slipped back into the country to play their role in one of the biggest and most complex military operations in Israel’s history.
The Origins of a Secret War
The Mossad made Iran its top priority in 1993 after Israelis and Palestinians signed the Oslo Accords on the White House lawn, seemingly ending decades of conflict.
Israeli Foreign Minister Shimon Peres, center-right — flanked by, from left, Israeli Prime Minister Yitzhak Rabin, Israeli negotiator Joel Singer, President Bill Clinton and Yasser Arafat, chairman of the Palestine Liberation Organization — signs the Oslo Accords in 1993. The agreement sought to end decades of conflict between the Israelis and Palestinians.
Credit:
J. David Ake/AFP via Getty Images
Israel had long had a complicated relationship with Iran. For decades, it maintained a strategic alliance with the shah of Iran. But Ayatollah Ruhollah Khomeini and the Islamists who overthrew the monarch in 1979 described the Jewish state as a “cancerous tumor” that should be excised from the Middle East.
Israel’s strategy is, in effect, to protect its nuclear monopoly in the region. It does not publicly acknowledge its arsenal, estimated at more than 90 warheads. The Israeli air force destroyed Iraq’s nuclear reactor in 1981 and a Syrian reactor under construction in 2007.
After the Iraq airstrike, Israel’s prime minister, Menachem Begin, declared that his country had a right to prevent neighbors from building their own bomb. “We cannot allow a second Holocaust,” he said.
Israeli Prime Minister Menachem Begin, left, in 1981 with Ariel Sharon, who at the time was the defense minister and would become prime minister in 2001. Begin said that his country had a right to prevent its neighbors from building a nuclear bomb.
Credit:
STF/AFP via Getty Images
A few years later, Iran began researching nuclear weapons, drawing on the expertise of a Pakistani engineer, Abdul Qadeer Khan, who had once worked for a Dutch company that produced enriched uranium.
Shabtai Shavit, the Mossad director whose term ended in 1996, said Israel was aware of Khan’s travels in the region but did not initially detect his crucial role in Iran’s program. “We didn’t fully understand his intentions,” Shavit told us in an interview before his death in 2023. “If we had known, I would have ordered my combatants to kill him. I believe that could have reversed the course of history.”
According to United Nations nuclear inspectors, the Iranians used blueprints provided by Khan to begin building the centrifuges needed to enrich uranium they purchased from Pakistan, China and South Africa.
In 2000, Shavit’s successor drew up plans for the Mossad’s special missions unit known as Kidon — Hebrew for “bayonet” — to assassinate Khan while he was visiting what one official described as “a Southeast Asian country.” The mission was shelved when Pakistan’s president, Gen. Pervez Musharraf, told President Bill Clinton he would rein in Khan’s global activities.
Iran turned to Abdul Qadeer Khan, a Pakistani engineer who had worked for a Dutch company that produced enriched uranium, as Iran began researching nuclear weapons.
Credit:
Robert Nickelsberg/Getty Images
That promise wasn’t kept.
That same year, the Mossad discovered that the Iranians were building a secret enrichment plant near Natanz, a city about 200 miles south of Tehran. The spy agency tipped off an Iranian dissident group, which went public with the revelation two years later.
Mossad veterans said that operatives — likely Israelis posing as Europeans installing or servicing equipment — walked around Natanz wearing shoes with double soles that collected dust and soil samples. Testing eventually revealed that the Iranian-made centrifuges were enriching uranium well beyond the 5% level needed for a nuclear power plant. (Medical isotopes use 20% enriched uranium; bombs need 90%.)
In 2001, Israel elected Gen. Ariel Sharon, famous for his belligerent toughness, as prime minister. The following year, Sharon named one of his favorite generals, Meir Dagan, as director of the Mossad. Both had a reputation for pushing boundaries and defying norms.
Dagan, who led the Mossad from 2002 to 2011, decided to make stopping Iran’s nuclear program the spy agency’s main goal.
Like Begin, who was born in Poland, Dagan was haunted by the Holocaust. Heads of foreign intelligence agencies recalled visiting his office and seeing a photograph of Nazi soldiers brutalizing Dagan’s grandfather on the wall. Explaining the photo’s meaning at an anti-Netanyahu rally in 2015, he said: “I swore that that would never happen again. I hope and believe that I have done everything in my power to keep that promise.”
Meir Dagan, who led the Mossad from 2002 to 2011, had this photograph of Nazi soldiers brutalizing his grandfather on the wall of his office. He explained its meaning in 2015: “I swore that that would never happen again. I hope and believe that I have done everything in my power to keep that promise.”
Credit:
Yad Vashem
Under Dagan’s leadership, the Mossad organized an array of covert operations to slow the Iranian program. Israeli agents began assassinating Iran’s nuclear scientists, sending operatives on motorcycles to attach small bombs to cars in traffic.
The Art of Recruitment
Dagan took pride in the Mossad’s growing ability to recruit Iranians and others for covert operations inside Iran.
One key to the spy agency’s success is the ethnic composition of Iran. Israeli officials noted in interviews that roughly 40% of the country’s population of 90 million is made up of ethnic minorities: Arabs, Azeris, Baluchis, Kurds and others.
Shortly before he died in 2016, Dagan told us that “the best pool for recruiting agents inside Iran lies within the country’s ethnic and human mosaic. Many of them oppose the regime. Some even hate it.”
Present and former officials said Dagan championed the shift to relying on foreign-born agents. In the early years of the effort to penetrate Iran, the spy agency had relied mostly on Israelis, known to Mossad insiders as “blue and white” — a reference to the colors of Israel’s flag.
Under Dagan, the Mossad’s leadership came to believe they could find highly effective agents in Iran or among Iranian exiles and others living in one of the seven countries that border it.
Meir Dagan, seen in an undated photograph, was a proponent of using foreign-born agents for the Mossad’s missions against Iran.
Credit:
Yaakov Saar/GPO/Getty Images
Present and former officials said the recruits fell into two categories. Some gravitated to the realm of traditional espionage, gathering intelligence and passing it on to their handler. Others expressed a willingness to carry out violent operations, including attacks on nuclear scientists.
Not surprisingly, given the risk of summary execution, many had initial doubts.
“Convincing someone to betray their country is no small feat,” said a former senior Mossad officer who oversaw units handling foreign agents. “It’s a process of gradual erosion. You start with a minor request, an insignificant task. Then another. These are trial runs. If they perform well, you assign them something larger, more meaningful. And if they refuse — well, by then you have leverage: pressure, threats, even blackmail.”
Spymasters, he said, try to avoid threats or coercion. “It’s better to guide them to a place where they act willingly — where they take the first step themselves,” the former officer said.
The most critical element is trust. “Your agent must be loyal and emotionally tied to you. Like a soldier who charges forward despite the danger, trusting his comrades, so it is with agents. He goes on the mission because he trusts his handler and feels a deep sense of responsibility toward him.”
Most of the people who agreed to work for Israel expected payment for the risks they were taking. But the present and former officials said the driving force for people who agree to spy on their own country is often more primal.
“Financial reward is, of course, important,” the former Mossad officer said. “But people are also driven by emotion — hatred, love, dependence, revenge. Yet it always helps when the recruit’s motives are supported by some kind of tangible benefit: not necessarily a direct payment but some type of indirect help.”
This is how S.T. was recruited.
His handlers said he was consumed by hatred toward the regime and what had been done to him by the Basij militia. But what finally pushed him to cooperate was the Mossad’s offer to arrange medical treatment unavailable in Iran for a relative.
For decades, medical care has been one of the Mossad’s signature recruitment methods. Israeli intelligence has links with doctors and clinics in several countries, and arranging surgery and various therapies was also used to penetrate Palestinian extremist groups. It has featured even more in approaches to Iranians, in the hope of persuading them to help Israel.
The Mossad also uses the internet to attract agents, creating websites and publishing social media posts aimed at Iranians that offer to help people suffering from life-threatening illnesses such as cancer. These posts include phone numbers or encrypted contact options.
Israeli intelligence can mobilize its international network to find trusted doctors or clinics — places that won’t ask too many questions. The Mossad typically pays the bills directly and discreetly.
Another incentive used to entice potential spies is higher education in a foreign country. Based on years of research and experience, Mossad recruiters know that Iranians crave access to quality education. Even the fundamentalist religious regime of the current supreme leader, Ayatollah Ali Khamenei, encourages academic advancement. This makes offers of placement in Western universities, or boarding schools for teenagers, an especially compelling tool.
Once a candidate is identified, the Mossad sets up an initial meeting in an accessible location — often in neighboring countries such as Turkey, Armenia or Azerbaijan, which are relatively easy for Iranians to enter. Other options include destinations in Southeast Asia like Thailand and India that allow Iranian citizens to apply online for business, medical or tourist visas.
Candidates undergo a series of meetings and psychological evaluations. Psychologists observe their behavior, often from behind one-way mirrors. They fill out detailed questionnaires about their personal history, including intimate details about their family life, and are questioned by a polygraph examiner.
Agents are regularly retested after they begin working in the field. Every action, whether minor or major, is followed by another lie detector test to confirm continued loyalty.
They receive extensive training and supervision. To avoid arousing suspicion, they are told what to wear, where to buy their clothing, what cars to drive, and even how, when and where to deposit the money they receive.
The agent-handler relationship is critical, as a former Mossad operative who “ran” agents explained. In many cases, the handler is simultaneously confessor, babysitter, psychologist, spiritual mentor and surrogate family member.
The goal is to build a bond so strong that the agent feels safe and supported — comfortable enough to share even their deepest personal secrets, including their sexual relationships.
Any and all information about the agent can be valuable to the Mossad, either as a red flag marking a potential vulnerability to Iran’s secret police or another aspect of the agent’s life that the handlers can put to use. Among the key questions: Who’s in the person’s social circle? Can he or she use that relationship to the Mossad’s benefit?
The operatives who were assigned to assassinate nuclear scientists on the street received extensive training from Mossad case officers. They were taught to ride motorcycles and either shoot their targets at close range or plant explosives on their vehicles.
The intent was both to deprive the Iranian program of expertise and to discourage promising scientists from working on nuclear weapons. From 2010 to 2012 the Israelis killed at least four scientists and barely missed another.
The operations were managed by Israelis, down to the smallest details, often from nearby countries or directly from Mossad headquarters north of Tel Aviv, and occasionally by Israeli intelligence officers who briefly entered Iran.
Operation Rising Lion
Over the years, the Mossad and Israel’s military repeatedly drew up plans to halt Iran’s nuclear program by bombing its key facilities. Israel’s political leaders always drew back under pressure from American presidents who feared an attack would trigger a regional war, destabilizing the Middle East. Hezbollah, Iran’s proxy in Lebanon, had stockpiled tens of thousands of missiles, enough to overwhelm Israel’s air defenses and hit its largest cities.
Those calculations shifted dramatically in the past year.
In April and October of 2024, Iran fired missiles and drones directly at Israel. Nearly all were shot down with the help of the United States and allies. The Israeli air force responded with airstrikes that destroyed much of Iran’s air defenses.
The remains of an Iranian missile ended up near the Dead Sea in Israel on Oct. 2, 2024.
Credit:
Erik Marmor/Getty Images
The Israeli military had begun planning a bombing campaign against Iran in mid-2024 that it hoped would be ready within a year. With Donald Trump’s victory in the November election, and Hezbollah neutralized, Israeli officials saw a window of opportunity.
Israel’s American-trained pilots had been secretly flying over Iran since 2016 — learning the landscape and exploring various routes to minimize the chances of detection.
One nuclear target in Iran, however, was considered so formidable that the Israeli air force had no plan for destroying it. The Iranians had built a uranium-enrichment facility at Fordo and buried it inside a mountain — nearly 300 feet beneath the surface. Iran tried to keep Fordo a secret, but the Mossad and American and British intelligence were able to track movements in and out of the mountain. President Barack Obama disclosed its existence in 2009, and United Nations inspectors who visited the site soon after found that Iran was planning for up to 3,000 highly advanced centrifuges to enrich uranium.
A 2013 satellite image shows a uranium-enrichment facility in Fordo, Iran.
Credit:
DigitalGlobe via Getty Images
Only the United States had a bomb powerful enough to pierce a mountain: the GBU-57 Massive Ordnance Penetrator, the world’s largest conventional bomb known as a “bunker buster.”
And so Israeli military planners drew up a plan for a highly risky ground operation, details of which are disclosed here for the first time. Under the plan, elite commandos were to be smuggled to the Fordo site without being detected. Then they would storm the building, taking advantage of the element of surprise. Once inside, their mission would be to blow up the centrifuges, grab Iran’s enriched uranium and escape.
The new head of the Mossad was skeptical. David Barnea, known as Dadi, had long pushed for aggressive actions against Iran. He had overseen the remote-machine gun attack in 2020 just before being promoted to the top job. Yet he thought the plans for a commando attack on Fordo were far too risky. Barnea worried that some of Israel’s best soldiers and spies would be killed or taken hostage, a nightmare for Israelis already deeply pained by the ordeal of Israeli hostages held by Hamas in Gaza since the attack of Oct. 7, 2023.
Barnea and other Israeli officials came to believe that the Trump administration might join an Israeli attack on Iran, with U.S. warplanes dropping the massive “bunker busters” on Fordo. Trump had repeatedly and publicly declared that he would not allow Iran to obtain a nuclear bomb.
The Man Running Israel’s Intelligence Operation
To prepare for what would be dubbed Operation Rising Lion, the Mossad and the military intelligence agency, Aman, stepped up their tracking of Iran’s military leaders and nuclear teams. Several of the operation’s planners said that Barnea significantly expanded the Mossad’s Tzomet, or Junction, division, which recruits and trains non-Israeli agents. The decision was made to entrust this foreign legion with Israel’s most sophisticated equipment for paramilitary operations and communications. The cover stories for each agent, known as their legends, were checked and rechecked for inconsistencies.
The Mossad’s espionage efforts were helped by a geographic fact. Iran is bordered by Iraq, Turkey, Azerbaijan, Armenia, Pakistan, Turkmenistan and Afghanistan. Smuggling is a way of life in the region, as thousands of people earn their living using donkeys, camels, cars and trucks to carry drugs, fuel and electronics across the borders.
The Mossad had developed contacts with smugglers — and often with the government intelligence agencies — in all seven nations.
“Bringing equipment in and out is relatively easy,” said an Israeli who has worked with Mossad on logistics, “and the Mossad also used front companies that legally shipped boxes and crates by sea and on trucks driven legitimately through border crossings.”
The material was delivered to “infrastructure agents,” Mossad operatives inside Iran who store the material until it’s needed. Mossad veterans said the gear can be hidden in safe houses for years, updated as technology evolves or maintenance is needed.
Officials said the Mossad trained the non-Israeli agents who would attack Iranian targets for about five months. Some were brought to Israel, where models had been built to enable practice runs. Others rehearsed their missions in third countries where they met Israeli experts.
There were two groups of commandos, each with 14 teams of four to six members. Some already lived in Iran. Others were anti-regime exiles who slipped into the country on the eve of the attack.
Each had their instructions, but they were also in touch with Israeli planners who could change or update the attack plan. Most of the teams were tasked with striking Iranian air defenses from a list of targets provided by the Israeli air force.
The Mossad had code names for each of the teams and their assignments, which were based on combinations of musical notes.
On the night of June 12, the teams arrived at their positions as orchestrated. The Israelis in charge of the covert operations directed the agents to leave little or no equipment behind. (Iranian media reports after the attack asserted that the infiltrators had missed their targets and fled without their gear; Israeli officials said what the Iranians found were insignificant components — the equivalent of gum wrappers.)
“One hundred percent of the anti-aircraft batteries marked for the Mossad by the air force were destroyed,” a senior Israeli intelligence official said. Most were near Tehran in areas where the Israeli air force had not previously operated.
In the first hours of the war, one of the commando teams struck an Iranian ballistic missile launcher. Israeli analysts believe this mission had a disproportionate impact, causing Iran to delay its retaliatory salvo against Israel out of fear that other missile launchers were vulnerable to attacks from inside Iran.
Officials emphasized that the military logistics of the plan were the work of Aman and the Israeli air force, which hit more than a thousand targets over the 11 days of airstrikes. But officials agree that the Mossad contributed key intelligence for one aspect of Rising Lion: the assassinations of senior Iranian commanders and nuclear scientists.
The Mossad compiled detailed information on the habits and whereabouts of 11 Iranian nuclear scientists. The dossiers even mapped the locations of the bedrooms in the men’s homes. On the morning of June 13, Israeli air force warplanes fired air-to-ground missiles at those coordinates, killing all 11.
After a delay, Iran retaliated with a barrage of missiles. Most were intercepted, but the ones that got through did considerable damage. Israel reported 30 civilian deaths and estimated its reconstruction costs at $12 billion. Iran’s state media put the death toll in their country at more than 600.
An aerial view of the destruction after an Iranian ballistic missile hit Ramat Gan near Tel Aviv, Israel, on June 14.
Credit:
Yair Palti/Anadolu via Getty Images
The question of how much Iran’s nuclear efforts were set back remains in dispute. Trump has insisted the American airstrikes on Fordo, Natanz and Isfahan “obliterated” Iran’s program. Analysts in Israeli and American intelligence have been more restrained.
“This war significantly set them back,” said a former head of Aman, Gen. Tamir Hayman. “Iran is no longer a nuclear threshold state, as it was on the eve of the war. It could be able to return to threshold status in one or two years at the earliest, assuming a decision by the Supreme Leader to break out toward a bomb.”
Hayman, who now heads the Institute for National Security Studies in Israel, said it’s possible the assault might have the opposite of its intended effect, if Iran becomes even more eager to build a bomb that could deter future Israeli attacks.
Yossi Melman is a commentator on Israeli intelligence and a documentary filmmaker. Dan Raviv is a former CBS correspondent and host of “The Mossad Files” podcast. They are the co-authors of “Spies Against Armageddon: Inside Israel’s Secret Wars.”
