DUBAI – Iran launched retaliatory missile strikes on Israel into Saturday morning, killing at least three people and wounding dozens, after a series of blistering Israeli attacks on the heart of Iran’s nuclear program and its armed forces.

Israel’s assault used warplanes, as well as drones smuggled into the country in advance, to assault key facilities and kill top generals and scientists.

Israel asserted the barrage was necessary before Iran got any closer to building an atomic weapon, although experts and the U.S. government have assessed that Tehran was not actively working on such a weapon before the strikes. It also threw talks between the United States and Iran over an atomic accord into disarray days before the two sides were set to meet Sunday.

Iran retaliated by launching drones and later firing waves of ballistic missiles at Israel, where explosions lit the night skies over Jerusalem and Tel Aviv and shook the buildings below. The Israeli military urged civilians, already rattled by the raging Israel-Hamas war in the Gaza Strip, to head to shelter for hours.

Iranian missiles strike Israel

Iran’s Supreme Leader Ayatollah Ali Khamenei said in a recorded message Friday: “We will not allow them to escape safely from this great crime they committed.” Iran’s U.N. ambassador said 78 people were killed and more than 320 wounded in Israeli attacks.

Iran launched waves of missiles at Israel late Friday and early Saturday.

A hospital in Tel Aviv treated seven people wounded in the second Iranian barrage; all but one of them had light injuries. Israel’s Fire and Rescue Services said they were injured when a projectile hit a building in the city. A spokesperson for Beilinson Hospital said one woman was killed.

Hours later, an Iranian missile struck near homes in the central Israeli city of Rishon Lezion, killing two people and injuring 19, according to Israel’s paramedic service Magen David Adom. Israel’s Fire and Rescue service said four homes were severely damaged.

Meanwhile, the sound of explosions and Iranian air defense systems firing at targets echoed across central Tehran shortly after midnight on Saturday. An Associated Press journalist could hear air raid sirens near their home.

Iran’s semiofficial Tasnim news agency reported a fire at Tehran’s Mehrabad International Airport, with a video posted on X of a column of smoke and orange flames rising from what the outlet said was the airport.

Israel’s paramedic services said 34 people were wounded in the barrage on the Tel Aviv area, including a woman who was critically injured after being trapped under rubble. In Ramat Gan, east of Tel Aviv, an AP journalist saw burned-out cars and at least three damaged houses, including one where the front was nearly entirely torn away.

U.S. ground-based air defense systems in the region were helping to shoot down Iranian missiles, said a U.S. official who spoke on condition of anonymity to discuss the measures.

Strikes raise fears of all-out war

Israel’s ongoing airstrikes and intelligence operation and Iran’s retaliation raised concerns about all-out war between the countries and propelled the region, already on edge, into even greater upheaval.

Countries in the region condemned Israel’s attack, while leaders around the globe called for immediate deescalation from both sides.

Israel had long threatened such a strike, and successive American administrations sought to prevent it, fearing it would ignite a wider conflict across the Middle East and possibly be ineffective at destroying Iran’s dispersed and hardened nuclear program.

But a confluence of developments triggered by Hamas’ Oct. 7, 2023, attack — plus the reelection of U.S. President Donald Trump — created the conditions that allowed Israel to finally follow through on its threats. Israeli Prime Minister Benjamin Netanyahu said the U.S. was informed in advance of the attack.

On Thursday, Iran was censured by the U.N.’s atomic watchdog for not complying with obligations meant to prevent it from developing a nuclear weapon.

Israel’s military said about 200 aircraft were involved in the initial attack on about 100 targets. Its Mossad spy agency positioned explosive drones and precision weapons inside Iran ahead of time, and used them to target Iranian air defenses and missile launchers near Tehran, according to two security officials who spoke on condition of anonymity.

It was not possible to independently corroborate the officials’ claims.

Among the key sites Israel attacked was Iran’s main nuclear enrichment facility in Natanz, where black smoke could be seen rising into the air. It also appeared to strike a second, smaller nuclear enrichment facility in Fordo, about 100 kilometers (60 miles) southeast of Tehran, according to an Iranian news outlet close to the government that reported hearing explosions nearby.

Israel said it struck a nuclear research facility in Isfahan, too, and said it destroyed dozens of radar installations and surface-to-air missile launchers in western Iran. Iran confirmed the strike at Isfahan.

Israel military spokesman Brig. Gen. Effie Defrin said the Natanz facility was “significantly damaged” and that the operation was “still in the beginning.”

Above-ground section of Natanz facility destroyed

U.N. nuclear chief Rafael Grossi told the Security Council that the above-ground section of the Natanz facility was destroyed. He said all the electrical infrastructure and emergency power generators were destroyed, as well as a section of the facility where uranium was enriched up to 60%, which is a short, technical step away from weapons-grade levels of 90%.

The main centrifuge facility underground did not appear to have been hit, but the loss of power could have damaged the infrastructure there, he said.

The first wave of strikes had given Israel “significant freedom of movement” in Iran’s skies, clearing the way for further attacks, according to an Israeli military official who spoke on condition of anonymity because he was not authorized to discuss details of the attack with the media.

Over the past year, Israel has been targeting Iran’s air defenses, hitting a radar system for a Russian-made air defense battery in April 2024 and surface-to-air missile sites and missile manufacturing facilities in October.

The official said Israel is prepared for an operation that could last up to two weeks, but that there was no firm timeline.

Among those killed were three of Iran’s top military leaders: one who oversaw the entire armed forces, Gen. Mohammad Bagheri; one who led the paramilitary Revolutionary Guard, Gen. Hossein Salami; and the head of the Guard’s ballistic missile program, Gen. Amir Ali Hajizadeh.

Netanyahu said the attack had been months in the making. In a video statement sent to journalists Friday, he said he ordered plans for the attack last November, soon after the killing of Hassan Nasrallah, the leader of Hezbollah in Lebanon, one of Iran’s strongest proxies. Netanyahu said the attack was planned for April but was postponed.

In its first response Friday, Iran fired more than 100 drones at Israel. Israel said the drones were being intercepted outside its airspace, and it was not immediately clear whether any got through.

Israel’s military said it called up reservists and began stationing troops throughout the country as it braced for further retaliation from Iran or Iranian proxy groups.

Trump urged Iran on Friday to reach a deal with the U.S. on its nuclear program, warning on his Truth Social platform that Israel’s attacks “will only get worse.”

“Iran must make a deal, before there is nothing left, and save what was once known as the Iranian Empire,” he wrote.

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Lidman and Frankel reported from Jerusalem.