How Israel carried out its largest ever attack on Iran

Israel’s wartime leaders, gathered in the bowels of the military headquarters in Tel Aviv, had just given the green light to the largest attack on Iran in Israel’s history—and the most politically dangerous. They called the operation ‘Days of Repentance’.

The attack was intended to punish Iran for attacking Israel, but was intended to prevent a full-scale war between the two enemies involving US forces and other countries in the region. The strike avoided oil and nuclear facilities that Iran had warned would lead to retaliation, appearing to heed the caution U.S. officials urged.

However, the attack marked a dangerous new phase in the confrontation between Israel and Iran, which began attacking each other directly earlier this year. It left Iran even more exposed to further airstrikes, with Israel destroying several of the Russian-made S-300 batteries, an Israeli official said.

“The message is that we don’t want an escalation, but if Iran decides to escalate and attack Israel again, it means we have increased our freedom of movement in Iranian airspace,” an Israeli official said.

For weeks, Israeli Prime Minister Benjamin Netanyahu had indicated that Israel would retaliate against Iran’s ballistic missile attack on Israeli territory on October 1. To pull off this attack, weeks of planning and delicate diplomacy were required.

Iran “knew Israel was coming, and yet they could not prevent anything,” said Assaf Orion, a retired Israeli brigadier general.

The US – sensing an opening after Israel killed Hamas leader Yahya Sinwar – has pushed for a ceasefire in Gaza. Secretary of State Antony Blinken visited Israel and other Middle Eastern capitals this week in an effort to reach an agreement that has eluded negotiators for months. The calibrated nature of the attack appeared to leave room for talks to continue, with negotiators due to meet in the Qatari capital Doha on Sunday.

But even as Israel pursued diplomatic channels that could end the war in Gaza and defuse tensions with Tehran, Israeli officials were finalizing the details of the retaliatory strike.

On Friday evening, as the sun set, marking the start of Shabbat, the Jewish day of rest, Israel’s Cabinet agreed in a phone call led by Netanyahu to go ahead with an attack that evening, an Israeli official said.

Hours before the attack began, Israel warned the US and several capitals of the Arab world and Europe about the nature and scale of the attack, according to people familiar with the matter. Officials in some of those countries then warned Iran.

The Israeli Prime Minister’s Office later said the idea that it informed Iran about the nature or timing of the attack was “false and absurd.”

When they finally began, the Israeli attacks unfolded in waves. The attack involved Israel’s most advanced air weapon, the F-35 fighter jets, which were adept at evading radar, people familiar with the mission said.

While the fighter jets were in the air, Israeli officials, aware that their American counterparts were frustrated that Israel had not warned last month that it would kill Hezbollah’s leader Hassan Nasrallah, also made it a point to actively inform their American counterparts about their attack.

Israeli Defense Minister Yoav Gallant called his American counterpart, Defense Secretary Lloyd Austin, who assured him of America’s readiness to defend Israel against pushback from Iran and allied militant groups.

The first batch of fighter jets destroyed air defense batteries in Syria and Iraq, clearing the flight path for the second and third flights to Iran.

Their exact route, which has not been shared by Israel, appeared to avoid airspace in Jordan after the Arab nation said it would not be part of an attack on Iran. Most of the attacks were launched from outside Iranian airspace, said Amir Aviv, a former senior Israeli military official who is often briefed by the defense establishment. Iran said Israeli planes attacked from Iraqi airspace, about 70 miles (110 kilometers) from the border.

The country’s military launched the second of at least three waves of attacks in Israel around 3:30 a.m., according to people familiar with the matter.

Israel’s attacks targeted Iranian facilities involved in the production of missiles, such as the cruise missiles and ballistic missiles that were targeted at Israel twice this year.

One of Israel’s hits took place at the vast Parchin military site, where Iran once worked on nuclear weapons capabilities, the UN atomic agency said. Four buildings were hit there, including three solid-propellant missile facilities, said Fabian Hinz, a researcher at the International Institute for Strategic Studies focused on Iran’s missile program.

Just before dawn, the Israeli military said the attack and retaliation had been completed. The planes returned without losses at the end of the four-hour attack.

Soon after, Iranian officials began telling Arab countries privately that the attack had hit locations with pinpoint accuracy. Publicly, the regime said it had caused “limited damage” and that Iran reserved the right to respond at a time of its choosing. Four Iranian soldiers were killed in the attacks, Iran said.

Israeli officials said they hoped the attack would end a tit-for-tat firefight with Iran and that the Israeli army could now focus on its war aims in the fight against Hamas in Gaza and the Lebanese Hezbollah, Iran’s allies .

Orion, the retired brigadier general, said the attack was calibrated but does not mean the end of tensions with Iran. “It gives both sides the opportunity to settle for now until the US elections, and then see where things go,” he added.

Anat Peled, Summer Said, Aresu Eqbali and Laurence Norman contributed to this article.