How the assault on Iran unfolded

The Iranian government supposedly drew painful lessons from the 12-day war with Israel and the United States in June.

After Israel located some of Iran’s top leaders and commanders deep underground during that war, Iranian security officials discovered that Israel had tracked them because their bodyguards were carrying cellphones.

Such failures had infuriated Iran’s supreme leader, Ayatollah Khamenei, according to Iranian and Israeli officials.

And yet, the fatal mistakes made by Iran this weekend were even worse than their missteps in June, making the latest assault on the nation’s leadership especially deadly.

Some of Iran’s highest military and intelligence officials gathered in broad daylight, above ground, at their last known address — the country’s National Security Council offices — for a high-level meeting Saturday morning, just as much of the world was expecting the United States or Israel, or both, to attack, Israeli defense officials said.

Even Khamenei — presumed to have been moving from one secret, underground hideaway to another — was above ground, at his anything-but-secret, official residential compound, the Israeli officials said.

Exactly how US and Israeli intelligence officials knew where all those leaders would be at 9:40 am local time Saturday is unclear. But the two countries exploited that knowledge and other sensitive intelligence collected from Iran to wage a three-wave attack that decimated the Iranian high command and quickly battered Iran’s air defenses, the defense officials said.

Next came a furious search-and-destroy mission against Iran’s ballistic missile systems, including munitions, launchers, crews, storehouses and production sites.

Crucially, in killing Khamenei, Israel also crossed a new Rubicon, killing the head of state of a sovereign country — something it had shied away from doing early in the war in June, according to two of the Israeli defense officials.

By midday Sunday, Israeli military officials said that air supremacy in the skies over Iran had been achieved and that its jets were flying freely over Tehran.

“Iran right now is totally exposed to airstrikes,” said Amir Eshel, a former commander of the Israeli air force. “It’s only for US forces and the Israeli air force to decide where, when and how. They almost cannot challenge. There’s almost total freedom of maneuver.”

Israeli officials were so emboldened by the freedom of action that some were privately expressing concerns — particularly after a deadly Iranian strike on a residential area west of Jerusalem on Sunday — that the United States wanted to bring the air offensive to a close too quickly. The Israeli air force still had many targets to eliminate, Israeli officials said.

“Ballistic missiles will take time,” said Zohar Palti, who headed the political-military bureau of Israel’s defense ministry after a long career in intelligence. “That’s not something that you finish today or tomorrow. Let’s try to finish, not to cut it short.”

“We need to get the time to clear out the ballistic missiles,” he added.

‘Black Sparrows’ and the Element of Surprise

Saturday’s attack depended on many factors. Chief among them was the element of surprise.

In the 12-day war in June, after a decision was made not to attempt to kill Khamenei during the initial strike, he disappeared and the opportunity did not arise again.

For that reason, the planners of Saturday’s strike calculated that any attempt to kill a senior Iranian official would have to be made in the first round, or they expected that precautionary measures would soon be taken, Israeli defense officials said.

In the war in June, Israel tried to kill additional Iranian officials on the last day of the fighting, according to Palti and an Israeli defense official, but was forced to call off that attack under pressure from President Donald Trump to stick to a ceasefire.

Ahead of Saturday’s strike, the military planned for months, looking for an opportunity in which military intelligence would learn in advance of a situation when top Iranian officials would be in the same place, according a separate Israeli defense official with knowledge of the plan.

Attacking in the morning hours, rather than at night — when Israel has launched prior campaigns against Iran — added to the tactical surprise this time, the official said.

A second wave of the attack immediately followed the Saturday morning strike on Iran’s leadership, with Israel targeting Iran’s surface-to-air missile batteries, especially those defending Tehran, Israeli defense officials said.

Although Israel had hit those systems in previous rounds of fighting and had boasted that they had destroyed them, the Iranians turned out to have restored some antiaircraft capacity since June, at least in part by producing some weapons themselves, according to a senior official updated with air force operations.

A key Israeli armament used Saturday morning, which also aided in the element of surprise, was a ballistic missile capable of being launched by F-15 fighter jets from far away.

It was originally developed as a practice-target missile for an Israeli antiballistic missile system, known as Arrow. But the new version, known as the Black Sparrow, allows for strikes on distant targets deep within Iranian territory, without requiring the jet to come within range of Iran’s surface-to-air missile batteries.

Israel first used such a missile in response to an Iranian attack in 2024, striking a radar system, defense officials said. Later, such missiles were used to paralyze Iranian surface-to-air batteries during Israeli attacks in November 2024, and then again in June, they said.

But they haven’t always achieved the desired result. On Sept. 9, Israel used such missiles to try to wipe out a group of Hamas leaders as they met in Qatar to discuss a ceasefire proposal by the Trump administration.

But the attack failed to kill senior Hamas officials and killed a member of Qatar’s internal security forces, ultimately forcing an apology from Israel, under pressure from Trump.

A ‘Strategic Ambush’ and Real-Time Hunting

During the third wave of Israel’s air offensive this weekend, the military deployed what it called its largest air armada in history, including some 200 planes.

Not since the Six-Day War in 1967, when Israel sent all but 12 of its planes to strike the Egyptian air force, had it dispatched so many aircraft on an attack mission.

Unlike previous operations, in which aircraft were sent in small waves, the Israeli air force mounted what it called a “strategic ambush.” In effect, Israel was “bringing the entire air force” to western and central Iran, an Israeli security official said.

The pilots’ mission: Destroy as many Iranian missiles as possible, as fast as possible.

The Americans, who joined in that hunt about half an hour after the Israelis first struck Iran’s leadership, focused on targets in eastern Iran, an area far from Israel but relatively close to American bases and forces. Israel took the country’s western half.

US forces also attacked the Iranian fleet, Trump said. “I have just been informed that we have destroyed and sunk 9 Iranian Naval Ships, some of them relatively large and important,” he wrote Sunday. “We are going after the rest — They will soon be floating at the bottom of the sea, also!”

With Iran’s air defenses so badly damaged, Israel was free Sunday to attack targets and symbols of the government in Tehran. The Israeli military said it had attacked “dozens of the regime’s military command centers, including headquarters belonging to the Islamic Revolutionary Guard Corps (IRGC), intelligence headquarters, IRGC Air Force command centers, and internal security headquarters.”

Israeli and American fighters are also hunting for Iran’s long-range ballistic missile launchers, two Israeli defense officials said, wary of the type of strike like the ones that killed Israeli civilians in Beit Shemesh on Sunday.

Eyal Hulata, a former Israeli national security adviser, said the level of US-Israeli cooperation in this weekend’s assault broke new ground.

“That’s a lot of effort by the intelligence communities in both countries to gather information, identify targets, understand where they are at a given time, and to do this on the fly, throughout the first day and so far on the second,” he said.

It’s “a level we haven’t seen before,” he added.