The airspace closings over Iran and Israel have affected thousands of flights.

Iran, in turn, has launched barrages of ballistic missiles and drones at Israel. At least three people have been killed and dozens wounded in the attacks.

It is the most intense fighting in decades between the two heavily armed countries, and has stirred anxiety over the prospect of an increasingly deadly conflict that could draw in the United States and other major powers.

The Israeli attack came as the United States and Iran were negotiating terms for a new diplomatic agreement to curb Iran’s nuclear program. Israel has argued that Iran — its main regional opponent — was making progress toward building a nuclear weapon, which Israel regards as an existential threat.

Residents of Tehran, Iran’s capital, reported hearing explosions on Saturday morning, and Iranian air defenses were activated. The Israeli military said it had conducted a wave of strikes against the air defenses around Tehran. The Iranian state news media said that the Israeli targets overnight had included a military jet hangar at Tehran’s Mehrabad airport.

Across Israel, people huddled in reinforced bomb shelters as air-raid sirens wailed outside, warning of incoming missile fire. Loud explosions reverberated overhead as Israel’s antimissile defenses intercepted many of the incoming missiles.

Israel has conducted roughly 150 strikes on Iran over two days, while Iranian forces have fired roughly 200 ballistic missiles at Israeli territory in addition to scores of drones, according to an Israeli military official.

Iran’s supreme leader, Ayatollah Ali Khamenei, said earlier that Iran was punishing Israel for the assault. The Islamic Revolutionary Guards Corps, a powerful Iranian state security body, said the targets were Israeli military sites used to attack Iran.

Prime Minister Benjamin Netanyahu of Israel has vowed that the campaign will last for “as many days as it takes” and told the Israeli public to prepare for a difficult struggle. He maintained in a video statement on Friday night that Iran had “never been weaker.”

Here’s what else to know:

• Dozens dead in Iran: Precise casualty figures in Iran could not be confirmed, but Iran’s ambassador to the United Nations, Amir Saeid Iravani, told the Security Council that Israel’s strikes had killed 78 people and injured about 300.

• Central Israel: On Saturday morning, at least two people were dead and about 19 injured in central Israel in the wake of an Iranian missile attack, according to Israeli health workers. Israel’s emergency service published footage from the scene showing heavily damaged homes that appeared to have been bombed. A third person was killed earlier during an Iranian missile barrage in Ramat Gan, a suburb east of Tel Aviv, the police said.

• Washington’s view: The United States’ possible role in the spiraling conflict remains unclear. While Israeli officials had hoped the Trump administration would participate in a joint attack, Secretary of State Marco Rubio denied U.S. involvement in the strikes. But President Trump also did not call for Israel to rein in its assault, and U.S. officials said they were moving warships and other military assets in the Middle East to help protect Israel and American troops in the region.

• Top Iranians killed: Two high-ranking military commanders, Mohammad Bagheri and Gen. Hossein Salami, were killed, Iran said, as was Ali Shamkhani, who had been overseeing the nuclear talks with the United States, officials said. Read more ›

• Nuclear sites: Rafael Grossi, the head of the United Nations’ nuclear watchdog, told the Security Council that Israel’s strike had destroyed the aboveground enrichment plant in Natanz, causing some chemical and radiological contamination. But he said the leak was “manageable.” He said the Iranian authorities had reported strikes on nuclear facilities in Fordo and Isfahan as well. Read more ›

Israel and Iran have closed their airspace since they began exchanging fire on Friday and Saturday, and neighboring Iraq, Jordan and Syria followed suit.

On Saturday, Iran’s state news media reported that Iran’s airspace would remain closed until 2 a.m. the next morning. And in Israel, Ben Gurion Airport remains closed until further notice. Israel’s three major airlines have also moved their fleets outside the country to prevent them from being damaged in Iranian airstrikes, the Israeli news media reported.

Jordan reopened its airspace at 7:30 a.m. on Saturday, and Syria’s Civil Aviation Authority also announced the full reopening of Syrian airspace to civilian air traffic. But the Iraqi Civil Aviation Authority said Iraq’s airspace would remain closed “in light of rising regional tensions.”

Some airlines canceled flights, while others altered their routes to avoid the conflict. Many carriers opted to fly over Saudi Arabia, while others flew over Turkey and Azerbaijan to avoid Iranian airspace, flight tracking data showed.

Emirates, a major carrier and Dubai’s flagship airline, canceled all flights to and connections via Iran, Iraq, Jordan and Lebanon until Sunday. FlyDubai, a budget carrier, suspended flights to 16 destinations.

In Lebanon, Middle East Airlines, the national carrier, suspended its flights on Friday, sending rumors swirling through the country that something terrible was looming, given that the airline had continued flying throughout the conflict with Israel last year. By Saturday afternoon, the airline said its flights would resume.

Lufthansa, Germany’s largest commercial airline, said it was canceling all flights to Tehran and Tel Aviv until July 31, while all flights to Amman, Beirut and Iraq’s Erbil airport were canceled until June 20. Delta Air Lines canceled all flights from Tel Aviv to New York until Aug. 31.

On Friday, Air India, which flies over the Middle East to reach destinations in Europe and North America, canceled or diverted more than a dozen flights. In some cases, it was operating alternative extended routes in a bid to avoid further cancellations, the carrier said on Saturday. Two days earlier, Air India suffered its own unrelated deadly disaster when one of its commercial flights crashed in Ahmedabad, India, killing more than 270 people.

The civil defense of the Palestinian Authority, which administers parts of the West Bank, said that its teams had responded to 40 reports of injuries and property damage from shrapnel falling in the West Bank on Friday. Seven children were among the injured, the civil defense said.

The latest escalation of violence in the region is adding to the fear and insecurity that many of the almost three million Palestinian residents in the West Bank already face living under Israeli military rule and a poorly managed Palestinian administration.

“It’s a terrifying experience,” said Yaqoub al-Rabi, 57, a resident of Biddya, a village near the border between the West Bank and Israel.

He was able to hear sirens at a nearby Israeli settlement in the West Bank blare late Friday, and he and six of his children and grandchildren crowded into his living room, crouching against a wall away from the windows.

But they did not feel safe, Mr. Rabi said. The most difficult part was seeing the fearful faces of his grandchildren as they heard powerful booms in the distance, he said.

While many Palestinians said they were fearful of the missiles, others said they had gone up to their rooftops to witness the spectacle of them flying overhead.

Maj. Gen. Anwar Rajab, the spokesman of the Palestinian Authority security forces, said Palestinians in the territory were encouraged to stay in their homes during missile attacks. The authority, he said, could not afford to build public shelters, noting that the governing body was facing a steep financial crisis.

Mohammed Abu al-Rub, the director of the Palestinian Government Communications Center, said that the West Bank lacked the technological infrastructure needed for the type of advance warning systems used in Israel.

“There are no sirens in the West Bank, because they require technologies and systems we simply don’t have,” he said.

Ala al-Khabass, 37, a resident of village outside Jenin in the northern West Bank, said the missiles were “frightening,” recalling a fragment of an Iranian missile that killed a Palestinian man in the West Bank town of Jericho in October when Iran fired a barrage of missiles at Israel.

“It’s horrifying, but what can we do?” he said. “The only thing we can do is accept we can’t do anything.”

“It is still unclear what decision we will make for Sunday,” Esmaeil Baghaei, a spokesman for Iran’s Foreign Ministry, was quoted as saying by Iran’s state news media.

After the initial round of Israeli attacks on Friday, the state news media said that the Islamic Republic was suspending its participation in the talks “until further notice.”

The senior Iranian figures killed by Israel included Ali Shamkhani, a former secretary of the Supreme National Council, who was overseeing the talks as part of a committee named by Iran’s supreme leader, Ayatollah Ali Khamenei.

Iranian officials described the killing of Mr. Shamkhani as targeting nuclear diplomacy.

Mr. Baghaei accused Washington of undermining the talks. The United States “acted in a way that makes dialogue meaningless,” he was quoted as saying, accusing Washington of claiming to want to negotiate while also giving Israel its consent to attack.

Although Washington has denied direct involvement, Mr. Baghaei said it was “unimaginable” for Israel to have carried out such “adventurous aggression” without a green light from the Americans.

“Basically, the Zionist regime’s constant desire was to drag Western countries into conflict and entanglement in the region,” he said. “It seems that it has succeeded this time as well and has somehow influenced a diplomatic process with this adventure. This actually shows that American policymakers are still heavily affected and influenced by this regime.”

President Trump and his administration have repeatedly urged Iran to continue with the dialogue as a means to halt further attacks.

“Iran’s leadership will be wise to negotiate at this time,” McCoy Pitt, a senior State Department official, said in a meeting of the United Nations Security Council on Friday focused on the crisis.

Mr. Trump has written on social media that even more brutal attacks are in store for Iran if it does not make a deal. Iran has denied seeking to develop nuclear weapons.

Leily Nikounazar contributed reporting.

Video filmed by a witness in Tehran and verified by The Times showed pillars of thick black smoke billowing from the part of Mehrabad airport where military hangars are positioned. The hangars appeared to be ablaze.

Perhaps because of that complacency, precautions that had been planned were ignored, the officials said.

This account of how Iranian officials were preparing before Israel conducted widespread attacks across their country on Friday, and how they reacted in the aftermath, is based on interviews with half a dozen senior Iranian officials and two members of the Revolutionary Guards. They all asked not to be named to discuss sensitive information.

Officials said that the night of Israel’s attack, senior military commanders did not shelter in safe houses and instead stayed in their own homes, a fateful decision. Gen. Amir Ali Hajizadeh, the commander of the Revolutionary Guards’ aerospace unit, and his senior staff ignored a directive against congregating in one location. They held an emergency war meeting at a military base in Tehran and were killed when Israel struck the base.

By Friday evening, the government was just beginning to grasp the extent of damage from Israel’s military campaign that began in the early hours of the day and struck at least 15 locations across Iran, including in Isfahan, Tabriz, Ilam, Lorestan, Borujerd, Qom, Arak, Urmia, Ghasre Shirin, Kermanshah, Hamedan and Shiraz, four Iranian officials said.

Israel had taken out much of Iran’s defense capability, destroying radars and air defenses; crippled its access to its arsenal of ballistic missiles; and wiped out senior figures in the military chain of command. In addition, the aboveground part of a major nuclear enrichment plant at Natanz was severely damaged.

In private text messages shared with The New York Times, some officials were angrily asking one another, “Where is our air defense?” and “How can Israel come and attack anything it wants, kill our top commanders, and we are incapable of stopping it?” They also questioned the major intelligence and defense failures that had led to Iran’s inability to see the attacks coming, and the resulting damage.

“Israel’s attack completely caught the leadership by surprise, especially the killing of the top military figures and nuclear scientists. It also exposed our lack of proper air defense and their ability to bombard our critical sites and military bases with no resistance,” Hamid Hosseini, a member of the country’s Chamber of Commerce’s energy committee, said in a telephone interview from Tehran.

Mr. Hosseini, who is close to the government, said Israel’s apparent infiltration of Iran’s security and military apparatus had also shocked officials. Israel has conducted covert operations in Iran against military and nuclear targets and carried out targeted assassinations against nuclear scientists for decades as part of its shadow war with Iran, but Friday’s multipronged and complex attack involving fighter jets and covert operatives who had smuggled missile parts and drones into the country suggested a new level of access and capability.

Iran’s supreme leader, Ayatollah Ali Khamenei, who has been moved to an undisclosed safe location where he remained in contact with remaining top military officials, said in a televised speech that Israel had, with its attacks, declared war on Iran. As he spoke, vowing revenge and punishment, Iran launched several waves of missile attacks on Tel Aviv and Jerusalem.

“They should not think they attacked and it is over,” Mr. Khamenei said. “No, they started it. They started the war. We will not allow them to escape from this crime unharmed.”

Earlier Friday morning, Iran’s Supreme National Security Council, a 23-person council responsible for national security decisions, held an emergency meeting to discuss how the country should respond. In the meeting, Mr. Khamenei said he wanted revenge but did not want to act hastily, according to two officials familiar with the discussions.

Divisions emerged on when and how Iran should respond, and whether it could sustain a prolonged war with Israel that could also drag in the United States, given how badly its defense and missile capabilities were damaged. One official said in the meeting that if Israel responded by attacking Iran’s infrastructure or water and energy plants, it could lead to protests or riots.

A member of the Revolutionary Guards briefed on the meeting said that officials understood that Mr. Khamenei faced a pivotal moment in his nearly 40 years in power: He had to decide between acting, and risking an all-out war that could end his rule, or retreating, which would be interpreted domestically and internationally as defeat.

“Khamanei faces no good options,” said Ali Vaez, the Iran project director of the International Crisis Group. “If he escalates, he risks inviting a more devastating Israeli attack that the U.S. could join. If he doesn’t, he risks hollowing out his regime or losing power.”

Ultimately, Mr. Khamenei ordered Iran’s military to fire on Israel. Initially, the plan was to launch up to 1,000 ballistic missiles on Israel to overwhelm its air defense and ensure maximum damage, according to two members of the Guards. But Israel’s strikes on missile bases had made it impossible to move missiles quickly from storage and place them on launchpads, they added.

In the end, Iran could only muster about 100 missiles in its first waves of attacks. At least seven sites were struck around Tel Aviv, killing one person and injuring at least 20 more, and damaging residential buildings.

On Friday, after Israeli attacks had somewhat subsided for part of the day, Iran’s military hurried to repair some of its damaged air defenses and install new ones, according to officials. Iran’s airspace remained closed with flights grounded and airports closed.

Some residents of Tehran spent Friday, a holiday, waiting in gas station lines to fill up their vehicles’ tanks and flocking to grocery stores to stock up on essentials like bread, canned food and bottled water. Many families gathered in parks late into the night, spreading blankets and picnics on the grass, and said in telephone interviews they feared remaining indoors after Israel had struck residential buildings in various neighborhoods targeting scientists and military and government officials.

Mehrdad, 35, who did not want his last name used because of fears for his safety, shared a video of his kitchen wall and windows destroyed when an Israeli missile struck the high-rise next door in his upscale neighborhood in northern Tehran. He said that he had been lucky to have been in the bedroom when the attack occurred, but some civilians in the neighborhood, including children, had been injured.

In the early hours of Saturday, Israel resumed its attacks on Tehran. Some residents, including Fatemeh Hassani, who lives in the Mirdamad neighborhood, said they heard drones buzzing overhead and nonstop explosion sounds followed by the rat-tat-tat of air defenses firing in eastern and central Tehran.

Mahsa, a 42-year-old computer engineer who lives in the capital’s north and similarly did not want to give her last name out of fear of her safety, said she and her family were unable to sleep. They not only could hear the booms but also could see traces of fire and smoke from their window.

“We are in the middle of a war, this much is clear to all of us, and we don’t know where it will go or how it will end,” she said.

“It was frightening,” said Noa Shekel, 23, who was taken out of a deep sleep when the sirens blared across Jerusalem.

Iran fired three waves of missiles at Israel on Friday night and Saturday morning, wounding dozens of people, including some seriously. The Iranian attacks came after Israeli strikes that targeted Iran’s nuclear sites and killed senior commanders.

In the shelter, signs of exhaustion were apparent: families lying on the floor, teenagers sleeping upright on the stairs, a pregnant woman slouching on a wooden bench.

Dozens of people — secular and religious Jews — were huddling in the shelter, which young people use as a community center on normal days.

For some, there was frustration that special weekend plans had been interrupted.

“We decided to spend Shabbat in Jerusalem to celebrate my daughter’s bat mitzvah,” said Rivkah Sharabi, 40, who was sitting beside her husband and their five children. “Instead, we’re spending it in a shelter.”

In the aftermath of the attack, some also spoke to The New York Times, sending voice notes amid flickering internet service and offering a glimpse of people’s experiences in a country where many don’t feel comfortable speaking to international news outlets. They described confusion, fear and anger against Israel, whose widespread attacks drew comparisons to the Iran-Iraq war of the 1980s.

‘We were not ready’

Shakiba, a 37-year-old occupational therapist based in Tehran, was only comfortable using her first name because of the heightened security situation in the country. She had been getting ready for bed at home with her two cats when the bombing began.

She looked outside and saw neighbors gathering on balconies and roofs, everyone trying to see what was happening. She added:

“The first sound was really shocking, because we were not ready, we were not expecting it. And it wasn’t just one sound — we heard a couple of sounds at the first. And I know all the people around the country and around the city were following the news, but we were not expecting it to happen.”

She later called two of her patients, an elderly couple who live alone, their children out of the country like many other Iranian families. They were near an area that came under attack, but their health conditions prevented them from leaving their home.

“The woman just cried by the phone, and she said that ‘I was really afraid because we can’t move’,” Shakiba recalled. She tried to reassure them, stuck in their home.

She also called another patient, a man with a neurological condition. He told her, “I’m OK now, but the sounds were so loud and so terrifying and I just felt that I am near to heart attack,” Shakiba said.

Describing the bombardment, Shakiba said that people like her patients — children with special needs, the elderly, frail and ill — had few resources to help them. “They are in shock,” she said.

Nor did she feel confident about her own plans. “I have two cats and they’re both heavy,” she said. “It sounds silly with everything going on, but I keep thinking about how I can evacuate with them if the need comes.”

‘Scenes of blood and flesh and burned feet’

Jila Baniyaghoob, a journalist and women’s rights activist in Tehran, said that there had been a large focus on Israel’s military targets, but that civilians had been harmed in the attacks as well.

She had a close friend at an apartment complex in the Saadat Abad district of Tehran, where residents include many faculty members from Tehran’s various universities, and which was struck during the attack early Friday.

A major fire spread after the attack, according to Ms. Baniyaghoob and photos of the scene.

Ms. Baniyaghoob said that she had heard most of the people killed in the strike were not members of the military or involved in Iran’s nuclear program. The exact toll of the attacks remained unclear on Friday night, although Iran’s Fars news agency, citing unofficial figures, said that dozens had been killed and more than 300 others injured.

Ms. Baniyaghoob said that her friend’s family had grabbed their young children and raced down stairwells to escape the complex. They passed “really awful scenes of blood and flesh and burned feet,” she said. “Most of the people who lived near the strike sites are feeling a collective fear, especially their children.”

‘The people are paying the price’

Bahman Ahmadi Amouee, an economic journalist, said he, along with many others, had been feeling optimistic before the attacks, noting that Iran was engaged in diplomatic talks with the United States and that there were hopeful economic signs within Iran.

But he believes the West and Israel took advantage of the circumstances, calling Israel’s leadership extremist and far right. “We’re seeing the same policy in Gaza, Lebanon, and Syria — policies that contradict with what the West says it values, like democracy and human rights.”

Mr. Ahmadi Amouee has written for newspapers that call for change within Iran and spent five years in Evin prison in 2009 amid a government crackdown on journalists.

In conflict with Israel, “the people are paying the price,” he said. “Once the stores open on Sunday, the prices will have undoubtedly gone up. There’s long lines of gas everywhere, people are nervous.”

He added:

“Whenever there’s war, or earthquake, or famine, people start feeling unstable, and the most vulnerable people in these situations are usually women, children and impoverished people. As soon as the markets open after the two day holiday, we’ll see the price of dollar going up, and the instability and lack of security will only multiply.”

The most dangerous kind of threat would arise from successful attacks on nuclear reactors. Over time, the splitting of atoms in reactor fuel results in buildups of highly radioactive spinoffs. Among the worst are Cesium 137, Strontium 90 and Iodine 131.

If Iodine 131 is inhaled or ingested, it ends up in a person’s thyroid gland. There, its intense radioactivity raises dramatically the risk of thyroid cancer, particularly in children. The other isotopes can also result in cancers.

But so far, no reports or evidence suggest that Iran’s nuclear reactors were hit in the Israeli attacks. Apparently spared were a power plant on the Persian Gulf, a research reactor in Tehran and a heavily guarded site ringed by antiaircraft weapons and miles of barbed wire.

Known as Arak, that isolated complex was long suspected of being built to produce plutonium, one of the two main fuels for atom bombs. But the Obama administration’s 2015 deal with Iran turned the complex into a nuclear relic unusable for that purpose. The Arak reactor never came to life.

A lesser threat to human health revolves around uranium, the other fuel of atom bombs. In recent years, Iran has focused on it with great intensity, building an increasingly wide array of industrial plants and complexes to refine the fissile element.

Uranium ore that miners dig up is relatively harmless. But it contains tiny amounts of a rare radioactive isotope, Uranium 235, that can be used to power nuclear reactors at low levels of enrichment, and to fuel atom bombs at higher levels. The percentage of U-235 in mined uranium is less than 1 percent.

The goal of uranium enrichment is to raise the percentage, which is often done through the use of centrifuges — machines that spin at extremely high speeds. Iran started with low percentages and, over decades, has increasingly raised its enrichment levels. The highest now stand at 60 percent, which is just short of bomb grade.

For human health, the higher the level of U-235 enrichment, the greater the danger. The isotope and its decay products emit three types of radiation: alpha particles, beta particles and gamma rays. The first two are relatively weak. Alphas cannot penetrate skin. Betas can be stopped by a layer of clothing.

But gamma rays are highly energetic and can penetrate the human body, damaging DNA and sowing the seeds of cancer. It takes thick concrete or lead to stop the penetrating rays.

Satellite images and expert analyses show that a main target of the Israeli strikes was the Natanz complex, the largest of Iran’s enrichment sites. Fully destroyed was the Pilot Fuel Enrichment Plant, where Iran was producing uranium enriched to near 60 percent. The images show a dark craterlike scar. And videos from a distance show clouds of dark smoke.

It’s possible that some of that smoke contained U-235 particles, which may pose a regional health hazard. But the International Atomic Energy Agency, which monitors the Iranian site, said it had so far detected no such danger.

“The level of radioactivity outside the Natanz site has remained unchanged and at normal levels indicating no external radiological impact to the population or the environment from this event,” Rafael Mariano Grossi, the agency’s director general, said Friday before the U.N. Security Council.

He mentioned concerns about alpha particles inside the Natanz facility, but called them “manageable” with appropriate radiation protection measures.

Acknowledging reports of attacks at Fordo and Isfahan, two other nuclear fuel sites in Iran, he said “we do not have enough information.”

Aside from the radiation danger, a complicating factor in the health calculus is that uranium in all its forms is a toxic heavy metal, similar to lead. If ingested it can produce a cascade of adverse health effects, with the kidneys a main target. Acute exposure can lead to renal failure. The main routes of exposure are ingestion of contaminated food and water, inhalation of airborne dust, and, to a lesser extent, contact with the skin.

The inhalation of uranium dust — a common hazard in mining and milling — is also a hazard. Inhaled particles can lodge in the lungs, leading to respiratory irritation, inflammation, and, over time, such lung diseases such as fibrosis.

A number of diplomats expressed their worries before the Council about the radiation threats from Israel’s strikes.

“We are particularly concerned by the potential radiological consequences,” said Vasily Nebenzya, Russia’s permanent representative to the U.N. They can lead, he added, “to the most dire consequences not just for the Middle East region, but for the world as a whole.”

Mr. Nebenzya said Russia was following closely the status of the inspectors in Iran of the I.A.E.A.

“The life and health of its personnel has been threatened,” he said. “And we expect that the director general of the agency is going to provide us with objective assessment and analysis of the developing situation, including from the viewpoint of radiological consequences.”