An extensive Israeli intelligence effort underpinned the Iran strikes.

Mr. Trump, whose administration has been holding nuclear talks with Iranian officials, said on Friday that Tehran “must make a deal, before there is nothing left.”

For years, Israel fought Iran’s proxy forces across the Middle East and more recently it has exchanged previous volleys of strikes with Iran. Yet Friday’s strikes were the first time it successfully hit Tehran’s nuclear facilities, including Iran’s main nuclear enrichment facility at Natanz, which a military spokesman said had suffered “significant damage.”

Iran’s supreme leader, Ayatollah Ali Khamenei, said that Israel “should anticipate a harsh punishment.” Later on Friday morning, the Israeli military announced that Iranian forces had fired about 100 drones at Israel, as Mr. Netanyahu vowed the fighting would last “as many days as it takes.” The Israeli military said it was working to intercept the Iranian attack, and there were no immediate indications of significant damage caused by the drones.

Here’s what else to know:

• Top Iranians assassinated: Mohammad Bagheri, the commander in chief of the military and the second-highest commander after the supreme leader, was killed, according to the Israeli military and Iranian media, as well as other top security officials. Ali Shamkhani, a leading politician who was overseeing the nuclear talks with the United States, was also killed, officials said. Mr. Khamenei moved quickly to appoint replacements, aiming to avoid the appearance of a leadership vacuum. Read more ›

• What was hit: In targeting the Natanz nuclear site, Israel struck at the beating heart of the Iranian nuclear program. The Israeli military said it had “caused significant damage” at Natanz and hit an underground compound housing centrifuges. Rafael Grossi, the chief of the International Atomic Energy Agency, said that there were no indications of attacks at two other major Iranian nuclear sites, the deep-underground uranium enrichment center at Fordow or the Isfahan nuclear fuel site.

• How it happened: Israel attacked at least six military bases around the capital Tehran, residential homes at two highly secured complexes for military commanders and multiple residential buildings around Tehran, according to four senior Iranian officials. Read more ›

• Tehran on edge: Residents of Tehran, the Iranian capital, reported hearing huge explosions, and Iranian state television broadcast images of smoke and fire billowing from buildings. Long lines were forming at gas stations and grocery stores. The Iranian government said that a number of civilians had been killed, including children, and dozens injured. Read more ›

• Threats to U.S. facilities: This week, the United States withdrew diplomats from Iraq, Iran’s neighbor to the west, and authorized the voluntary departure of the family members of U.S. military personnel from the Middle East. The U.S. military has a large fleet of warplanes, naval vessels and thousands of troops stationed in the region.

• Oil prices rise: Crude oil prices jumped sharply following the Israeli attack, with Brent crude jumping 9 percent to nearly $78 a barrel. Read more ›

It was a joint effort between Israeli military intelligence and the Mossad, code named “With the Strength of a Lion,” one of the officials said.

The people spoke on the condition of anonymity to discuss sensitive intelligence matters.

The Israeli intelligence apparatus has been at the heart of a series of operations aimed at Iran and its proxies in recent years.

Israel assassinated Iran’s top nuclear scientist, Mohsen Fakhrizadeh, with a remote-controlled gun in 2020, and assisted the United States killed Maj. Gen. Qassim Suleimani, Iran’s top security and intelligence commander, in a drone strike the same year.

In 2022, two assassins on motorcycles shot and killed Col. Sayad Khodayee, an officer in Iran’s Revolutionary Guards; Israel confirmed its role to the United States. Last year, Israel was able to kill Ismail Haniyeh, Hamas’s political leader, by planting an explosive device in a Tehran guesthouse run by the Islamic Revolutionary Guard Corps.

Israel also deeply penetrated Iran’s most powerful Iranian proxy, Hezbollah, leading to a spate of attacks in 2024. In September, it targeted members of the militia in elaborate, coordinated attacks using pagers and walkie-talkies, killing dozens of people and injuring thousands. It was also able to infiltrate the group’s communications, culminating in airstrikes the same month that killed the Hezbollah leader, Hassan Nasrallah.

In the attack on Friday, Israel targeted nuclear sites in Iran along with air defense as well as missile systems and storage facilities. The extent of the damage was unclear, but the Israeli military said it had struck Iran’s main nuclear enrichment facility at Natanz.

Here are the main centers of Iran’s nuclear program:

Natanz

Roughly 140 miles south of Tehran, Natanz is considered Iran’s main center for uranium enrichment, and it was a prime target of the Israeli strikes. The damage to it appeared to be severe. It is only partially underground and was recently reinforced.

It contains a range of sophisticated centrifuges, including the most advanced models, for enriching uranium to high levels. The International Atomic Energy Agency, the U.N. nuclear watchdog, says there are nearly 14,000 centrifuges at work there, with thousands more in place but inactive.

Uranium enriched at low levels can be used as fuel for civilian uses, such as producing energy. Highly enriched uranium can be used to make nuclear weapons.

Natanz has been targeted in the past, with a computer virus, Stuxnet, some 15 years ago, and with sabotage and explosions as recently as 2021. Iran has always in the past repaired the damage and increased the sophistication of its centrifuges.

Rafael Grossi, the head of the I.A.E.A., confirmed on Friday that Natanz had been hit but said that no radiation leak had been detected so far. He condemned attacks on nuclear facilities in general, as he has done in Ukraine, as very dangerous.

“Any military action that jeopardizes the safety and security of nuclear facilities risks grave consequences for the people of Iran, the region and beyond,” Mr. Grossi told the agency’s board of governors in Vienna.

Fordow

Iran’s best-protected nuclear site, Fordow, near the city of Qom, is deep inside a mountain, estimated to be about half a mile below ground to protect it from bombing. Israel did not appear to have attacked it.

To do so would require repeated use of huge “bunker buster” bombs, and most experts think that cannot be done by Israel alone, without American help.

Fordow was operated secretly by Iran until it was exposed in 2009. It contains Iran’s most advanced centrifuges and is considered crucial for Iran to enrich uranium to 60 percent, close to bomb grade. It is said to contain close to 3,000 sophisticated centrifuges, more than half of them the most modern type, with the capacity to install at least 1,000 more.

Parchin

Parchin is a military complex southeast of the capital, Tehran, where Iran has tested high explosives, which can be used as triggers for nuclear warheads. It is widely suspected that the site was used in the past by Iran in efforts to weaponize enriched uranium.

Iran has denied ever doing nuclear work there but has refused to allow the I.A.E.A. access it has demanded.

Bushehr

Bushehr is Iran’s only operating nuclear power plant. Located on the coast of the Persian Gulf, it uses Russian fuel that Russia then takes back when it is spent.

“I gave Iran chance after chance to make a deal,” he wrote on Truth Social, his social media platform, on Friday morning. “I told them, in the strongest of words, to ‘just do it,’ but no matter how hard they tried, no matter how close they got, they just couldn’t get it done.”

The negotiations had lasted only two months, and in recent weeks Mr. Trump had told Prime Minister Benjamin Netanyahu of Israel to hold off on any attack in order to let diplomacy play out. On Thursday afternoon, as Israel’s final attack preparations were underway, Mr. Trump told reporters, “I don’t want them going in” because “I think it would blow it” with the talks. (He immediately added that it “might help actually, but it could also blow it.”)

In his post, Mr. Trump suggested that some Iranian leaders who were opposed to a deal had been targeted in the Israeli attack, which killed several top Iranian military officials and at least two prominent nuclear scientists.

“Certain Iranian hardliner’s spoke bravely, but they didn’t know what was about to happen. They are all DEAD now, and it will only get worse!” Mr. Trump wrote.

During his first term, Mr. Trump pulled the United States out of a 2015 nuclear deal with Iran that was signed by President Barack Obama, deriding the agreement as “one-sided” and a “disaster.” It had allowed Iran to keep producing fuel at low levels, suitable for nuclear power plants but not for weapons — a position his own administration considered as recently as two months ago.

American and Iranian negotiators had been planning to meet on Sunday in Oman for a sixth round of talks. Those negotiations are now in limbo, with the Iranian government announcing on state television after the strikes on Friday morning that it would not participate in discussions with the United States on Sunday and until further notice.

Mr. Trump’s social media post attempted to put pressure on Iran to continue negotiating. “The next already planned attacks,” he wrote, would be “even more brutal.”

He added: “Iran must make a deal, before there is nothing left, and save what was once known as the Iranian Empire.” In his often-used capital letters, he concluded, “JUST DO IT, BEFORE IT IS TOO LATE.”

In the clearest sign of that weakened stance, the Lebanese militant group Hezbollah, seen as Iran’s most powerful proxy, condemned the Israeli attack in a statement but stopped short of vowing any military action in response — a notable omission from a group that has long served as the central pillar of the axis.

“The axis hasn’t been fully destroyed, but it has been significantly diminished beyond the point of return,” said Mohanad Hage Ali, a senior fellow at the Carnegie Middle East Center in Beirut. “It has been transformed into an axis of sitting ducks waiting for the next Israeli strikes rather than taking initiative and pushing Israel into the defense, as was the case just a few years ago.”

Iran fostered the web of armed groups — including Hamas, Hezbollah, the Houthis of Yemen and militias in Iraq — to enable them to carry out attacks on Israel and to provide Iran with valuable allies in the region that could serve as a deterrent against Israeli attacks on Iran itself.

After the deadly Hamas-led attacks in Israel on Oct. 7, 2023, and Israel’s devastating invasion of Gaza, many of those groups carried out their own strikes against Israel. But in the year and a half since, Israel launched audacious attacks on those militias in Lebanon, Syria, Yemen and Iran, and the response from the Axis has grown increasingly muted.

In Lebanon, Hezbollah is battered after its 14-month war with Israel that wiped out the group’s top brass, destroyed large chunks of its arsenal and left the country with a multibillion-dollar bill for reconstruction.

Its stinging defeat also spurred political momentum against the group, undoing its once iron grip on Lebanon’s politics, after many Lebanese blamed Hezbollah for dragging the country into one of its deadliest and most destructive wars.

“Beyond military limitations, Hezbollah’s political standing is also strained,” said Johnny Mounayar, a political analyst based in Beirut. “Domestically in Lebanon, opposition to Hezbollah has grown and even former allies are no longer aligned with it.”

The strongest arm of the axis now appears to be the Houthis, who control most of northwestern Yemen and have been launching rockets and drones at Israel and targeting ships in the Red Sea since October 2023, in what Houthi officials have characterized as a campaign of solidarity with Palestinians in Gaza.

Those attacks appeared to ramp up last month when a Houthi missile landed near a terminal of Israel’s main international airport. In response, Israel bombed the international airport in Yemen, which serves the capital, Sana, causing extensive damage and destroying the last remaining aircraft used by the Houthi government, according to Israeli officials.

The Houthis have still retained their ability to hit ships in the Red Sea, and last month they expanded their attacks on Israeli interests there to include vessels at or on their way to the port of Haifa.

A video taken by a witness and verified by The New York Times shows large plumes of smoke billowing from the airport in Tabriz as strikes continued to hit the area, to the gasps of onlookers.

Soon after, another alert instructed all citizens to stay close to protected areas and bomb shelters in anticipation of Iranian retaliation.

By breakfast time, the Israeli military said Iran had already begun its first wave of response, sending more than 100 drones in Israel’s direction.

All gatherings were banned. Schools remained closed. Israel felt strangely cut off from the world after its airspace was closed to civilian air traffic and all flights arriving at or departing from Ben-Gurion International Airport, near Tel Aviv, were canceled.

Many people were confused about how to proceed because officials had said on television that they should venture out only to pick up essential items. Some people had already headed out before dawn to stock up on food from 24-hour grocers and lined up at gas stations.

After 9 a.m., others were hurrying through the aisles of a Jerusalem supermarket, hoping to make it back home in the hour or so they thought they had before the drones might arrive from Iran.

Shoppers were stocking up on bottled water and there had been a run on eggs.

“I’m a little apprehensive, on the one hand,” said David Hazony, 56, an American Israeli writer who had just finished his shopping, adding that he has children who serve in the military reserves.

“On the other hand, there’s a strong sense of relief,” he said, referring to Israel’s offensive against Iran. “It’s something we knew needed to happen for decades, but I always had doubts that our leadership had the guts to do it,” he said.

Jawwad Abu Humous, 45, a manager at the supermarket and a Palestinian resident of East Jerusalem, said he had heard about the Israeli attack only when he got to work in the morning.

“We’ve heard ‘Iran, Iran’ for years,” he said. “In the end,” he added, “we want peace and quiet. War is hard for everyone.”

The military said it had begun intercepting the drones outside of Israeli territory. By 11 a.m., the instructions were relaxed. Citizens were no longer required to stay close to bomb shelters but were told they could go out, get some air — and stock up on food.

Rafael Grossi, the head of the U.N. nuclear agency, said that so far there are “no elevated radiation levels” detected around the Natanz nuclear site. He also said there were no indications of attacks so far at two other major Iranian nuclear sites, the deep-underground enrichment center at Fordow or the Isfahan nuclear fuel site, where much early processing of nuclear fuel takes place. Isfahan is also suspected of being a core location for secret nuclear weapons research, American officials say.

Israeli strikes targeted Natanz, the major nuclear facility near the city of Isfahan; the Parchin military base near Karaj. At least a dozen military bases, missile depots and nuclear and military research centers in multiple cities across Iran were hit.

Israel also struck residential buildings in densely populated neighborhoods of Tehran, in affluent, middle-class and working-class neighborhoods, according to witnesses, videos, photos and Iranian state media.

Iranian officials had dismissed the warning signs that Israel was planning to strike nuclear sites as propaganda and a media frenzy aimed at pressuring Tehran into concessions in talks with the United States over curbing its nuclear activities.

The government advised people to stay calm. But there was no sign of any measures to provide shelter and no guidance to the public on safety if more attacks were to come.

Fatemeh Hassani, a Tehran resident who lives in the affluent neighborhood of Pasdaran, said she and her husband and children were startled awake by an extremely loud boom, followed by another, and then another. Only when she checked her phone to see whether it was a thunderstorm did she learn that it was an attack.

Ms. Hassani said she huddled with her children away from the windows.

Across the city, Mohammad Jamali, standing on a roof near Chitgar Lake, said he could see jets approaching a military base and then a large fire and smoke billowing in the air.

Sara, a 52-year-old mother of two in Tehran, said it was a very scary night.

“We woke up with our house shaking from the explosions, and it hasn’t stopped,” said Sara, who asked to be identified by her first name only.

Mehdi, a resident in the Sadaat Abaad neighborhood, where an apartment building had collapsed, said neighbors had spilled into the streets with children in their pajamas clinging to their parents, looking dazed.

When dawn broke, the attacks had not stopped. But residents and local journalists in Tehran were in the streets anyway, taking stock of the damage.

State television reporters did live broadcasts from targeted neighborhoods. Some apartment buildings were shown half standing, and in one instance, an entire floor was blown out. In another, the roof of several buildings had pancaked and debris, shredded glass and mangled metal covered the streets.

Ali, a 42-year-old businessman who has a toddler and lives in a high-rise in northern Tehran, said in a telephone interview that he and his wife were rattled by the attacks on residential buildings, including one in their neighborhood. He was considering leaving the city for the countryside for a few days.

Some called for revenge.

At the Jamkaran mosque in the city of Qom, a crowd of government supporters gathered early Friday chanting, “Death to Israel,” and “Death to America,” according to state media.

The attack on the Natanz nuclear site closed down a major highway connecting Tehran to Isfahan, state media reported. The cities are roughly 200 miles apart.

Some Iranians feared the country was heading into an all-out war. And with air defenses taken out and military commanders killed, they wondered how the country could sustain a prolonged conflict.

Here is what we know about those killed:

Military Generals

• Maj. Gen. Mohammad Bagheri, chief of staff of the armed forces and the second-highest commander after Ayatollah Khamenei. He was replaced by Maj. Gen. Abdolrahim Mousavi, according to Iranian state news agency IRNA.

• Gen. Hossein Salami, commander in chief of the Revolutionary Guards, Iran’s primary military force. He was replaced by Gen. Mohammad Pakpour, IRNA reported.

• Gen. Gholamali Rashid, deputy commander in chief of the armed forces.

• Gen. Amir Ali Hajizadeh, the head of the airspace unit of the Revolutionary Guards.

Politicians

• Ali Shamkhani, one of Iran’s most influential politicians and a close confidant of Mr. Khameini, was killed, according to three senior officials and Iranian media reports. He had been overseeing nuclear talks with the United States as part of a committee named by Mr. Khamenei to direct the negotiations.

Nuclear Scientists

• Fereydoun Abbasi, the former head of the Atomic Energy Organization of Iran.

• Mohammad Mehdi Tehranji, a theoretical physicist and president of the Islamic Azad University in Tehran.

Israel also said that it had killed the top military leadership of Iran, confirming reports from Iran state media and officials. Among those killed were Mohammad Bagheri, the Iranian chief of staff and Hossein Salami, the head of the Islamic Revolutionary Guards Corps.

There are no reports yet of whether Iran’s other major enrichment site, called Fordow, was targeted as well. It is a much harder target, buried deep under a mountain, deliberately designed to be out of Israel’s reach.

As a result, it may take days, or weeks, to answer one of the most critical questions surrounding the attack of Iran’s facilities: How long has Israel set back the Iranian nuclear program? If the program is delayed only a year or two, it may look as if Israel has taken a huge risk for a fairly short-term delay. And among those risks is not only the possibility of a long-lasting war, but also that Iran will withdraw from the Nuclear Nonproliferation Treaty, take its program underground, and race for a weapon — exactly the outcome Mr. Netanyahu was out to prevent.

History suggests such attacks have unpredictable results. Even the most ingenious attack on the program 15 years ago — a cyberassault that put malware into the system, destroying centrifuges — only slowed Iran for a year or two. And when the program came back, it was bigger than ever.

Over nearly 20 years, Israel and the United States have targeted the thousands of centrifuges that spin inside the Natanz facility, in hopes of choking off the key ingredient Iranian scientists needed to build a nuclear arsenal. Together the two countries developed the Stuxnet worm, the cyberweapon intended to make the centrifuges spin out of control. That operation, code named Olympic Games, was born in George W. Bush’s administration and flourished in Barack Obama’s until the operation was exposed.

Then Israel sabotaged buildings that produced critical parts for the centrifuges, and began assassinating scientists key to the operation. But those were temporary setbacks. Iran recovered quickly. And the centrifuges at Natanz continued to spin, until the 2015 nuclear deal with Tehran forced the country to give up 97 percent of its fuel and slow the enrichment at Natanz to a crawl. That agreement also capped the level of enrichment to a level useful for generating nuclear power but not sufficient to make a bomb.

For three years, it seemed like the threat posed by Natanz had been contained. Most American officials believed that while the agreement had not terminated the program, it had contained it. The output of the Natanz plant was minimal.

But then President Trump pulled the United States out of the accord in 2018, calling the deal a disaster. And within a few years, Iran began revving up the facility, and putting new, far more efficient centrifuges in place. It increased enrichment levels to 60 percent purity — just shy of bomb grade. Experts said it would take only a few weeks to further raise the level to 90 percent, commonly used in atomic weapons.

Iran also made other moves that painted an even bigger target on Natanz. Over the past few months, international inspectors have concluded, Iran sped up its enrichment. On Thursday night — Friday morning in Israel — Mr. Netanyahu used its recent progress to argue that Iran now has enough fuel for nine weapons and that the country could “weaponize” that fuel within a year. That accords with what inspectors reported a week ago.

Mr. Netanyahu made the argument in an address to the Israeli people that the intelligence suggested the risk to Israel of not acting was too high. That judgment will be long debated — along with the question of whether the diplomacy that Mr. Trump had underway might have contained Iran’s capability, as the accord a decade ago did.

But it is still too early to know how much damage Israel did. Natanz is not deeply buried, but the centrifuge halls are 50 yards or more beneath the desert, and covered by highly reinforced concrete. The question is whether the centrifuges were destroyed.

Israel’s attacks went beyond the facilities. It also sought to decapitate both the military and nuclear leadership.

For years, Israel targeted top nuclear scientists individually. Some were killed by sticky bombs attached to their car doors. The country’s chief nuclear scientist was killed in a robot-assisted assassination. But some of the strikes Thursday night appeared to wipe out their headquarters and living spaces, part of an apparent effort to kill the personnel en masse.

One mystery still surrounding the attack is whether Israel made any attempt to hit the deepest, most protected facility among its sprawling nuclear complexes: the enrichment center called Fordow. It is on an Islamic Revolutionary Guards Corps base, and is deep within a mountain — nearly a half-mile under the surface, according to Rafael Mariano Grossi, the director general of the International Atomic Energy Agency, who has visited the site.

“If you don’t get Fordow,” Brett McGurk, who has served as Middle East coordinator for several American presidents of both parties, “you haven’t eliminated their ability to produce weapons-grade material.”

American officials have said Israel does not have the bunker-busting bombs to get at that facility, where Iran’s most advanced centrifuges have been installed. And if Fordow survives the attacks, then there is a good chance the key technology of the country’s nuclear program will survive with it.

Israel has a history of successfully assassinating Iranian security officials and nuclear scientists. But it has generally picked them off one by one in covert operations as part of its long shadow war with Iran and in Lebanon or Syria.

The strikes early on Friday proved to be a stunning escalation of that tactic. Not only did they target Iran’s nuclear program and air defenses, the Israeli attacks also eliminated the top tier of military commanders all at once, targeting their residential homes, including some in secure military complexes. In some areas of the capital, Tehran, entire apartment buildings collapsed.

Gen. Hossein Salami, the commander of the Islamic Revolutionary Guards Corps, was killed in an Israeli strike within Tehran, the Revolutionary Guards said in a statement. General Salami was killed alongside a number of other members of the security body, it said.

Iran’s supreme leader, Ayatollah Ali Khamenei, who is also the commander in chief of all armed forces, said in a statement read on state television said that Israel “should anticipate a harsh punishment. The strong hand of the Islamic Republic will not let them go.” He added that a number of senior military commanders and nuclear scientists had been killed in attacks that included residential targets. “The Zionist regime with this crime has created a dark and painful fate for itself, and it will definitely receive it.” Mr. Khamenei did not mention the United States in his statement.

Iran had not been attacked by a foreign enemy with such sweeping force since 1989 when the country was at war with Iraq. Mr. Khamenei had made averting war a central part of his legacy, taking the country to the brink of conflict several times, including twice with Israel last year, but stopping short of an all-out war.

That calculation appeared to have ended on Thursday night as Iranian officials openly said the country was preparing for war. But that effort is likely to be severely hobbled by the heavy blows to Iran’s chain of command and the air defenses that protect key military, nuclear and strategic sites.

Four Iranian officials said Israel had attacked at least a dozen military bases, missile depots, nuclear and missile bases, in multiple cities in Iran including Tehran, Tabriz, Isfahan, Kermanshah and Arak. Natanz nuclear site was also severely damaged, according to state television, and the damages extended to a major highway connecting Tehran to Isfahan.

“Unfortunately they did what we did not think they would do,” said Mehdi Rahmati, a conservative political analyst in Tehran close to the government in an interview after the attacks. “Iran will be responding very seriously aiming to inflict destruction, we anticipate a period of pingpong attacks that could spread to the region.”

In addition to the military commanders, Ali Shamkhani, a senior former navy commander, and one of Iran’s most influential politicians and a close confidant of Mr. Khamenei was also killed after sustaining severe injuries in an attack on his penthouse apartment in a residential luxury tower in northern Tehran, according to three senior officials and Iranian media reports.

Mr. Shamkhani, former secretary of the Supreme National Council, was overseeing the nuclear talks with the United States as part of a committee named by Mr. Khamenei to direct the negotiations. Killing him, officials said, was targeting efforts at nuclear diplomacy.

At least three other senior Iranian figures were thought to have been killed, according to Iranian state media. They were Gen. Gholamali Rashid, a senior leader in the Iranian armed forces; Mohammad Mehdi Tehranji, an Iranian physicist; and Fereydoun Abbasi, an Iranian nuclear scientist.

As leader of the Guards force, General Salami was responsible for securing Iran’s borders and safeguarding it against any foreign attacks. The Revolutionary Guards spokesman vowed to “respond decisively and harshly to the aggression of the Zionist enemy” and deliver a decisive blow to Israel and the United States following his death.