by Yossi Melman and Dan Raviv for ProPublica

ProPublica is a nonprofit newsroom that investigates abuses of power. Sign up to receive our biggest stories as soon as they’re published.

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 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.

© ProPublica