Trump says he is ‘not happy’ with Israel and Iran.

Mr. Netanyahu’s office said that Iran had fired missiles after the cease-fire took effect, and that the Israeli military had retaliated by striking a radar system near Tehran. Iran’s military denied violating the cease-fire, and Mr. Netanyahu’s statement indicated that Israel’s retaliation was limited. That appeared to suggest that the two sides — both of which claim to have prevailed in the conflict — want the truce to hold. In a Truth Social post, Mr. Trump said that Israel “is not going to attack Iran” and that “all planes will turn around and head home.”

Mr. Trump’s comments came before he left Washington for a NATO summit in the Netherlands. The truce, if it holds, could give him a chance to claim a diplomatic achievement in a conflict that had threatened to escalate.

Over the weekend, Mr. Trump ordered U.S. forces to bomb Iranian nuclear sites, prompting Tehran to respond by firing missiles at an American base in Qatar on Monday. Hours after Iran fired the missiles, which were intercepted, Mr. Trump abruptly announced a cease-fire between Israel and Iran, with few details, catching even some of his own officials by surprise.

Here’s what else to know:

• Global reaction: The cease-fire announcement was welcomed, albeit cautiously, by world leaders. “If a cease-fire has indeed been achieved, then that can only be welcomed,” said Dmitri S. Peskov, the Kremlin spokesman. President Emmanuel Macron of France praised the cease-fire announcement but warned that “the situation remains volatile and unstable.”

• Trading fire: Before the cease-fire took effect, the Israeli military said it had struck missile launchers in western Iran that had been poised to fire at Israel. Iran launched at least four barrages of ballistic missiles at Israel. At least four people were killed when a missile hit an apartment building in the southern city of Beersheba. In Tehran, residents said they endured a night of the heaviest airstrikes since the war began June 13.

• Diplomacy: Qatar intervened on behalf of the Trump administration and persuaded Iran to agree to a cease-fire with Israel, according to three diplomats briefed on the matter. Mr. Trump had asked for Qatar’s help and the Qatari prime minister, Sheikh Mohammed bin Abdulrahman Al Thani, then persuaded Iran to agree to the proposal in a call with the Iranian leadership, the diplomats said. The details of the cease-fire understandings remain unclear.

• Investors relieved: News of the cease-fire sent markets higher in Asia, where countries need energy imports to power their economies. Stocks in South Korea surged the most at 3 percent. S&P 500 stock futures were about 1 percent higher, signaling an expected rise when trading begins in New York. The price of oil has fallen back to around where it was before Israel first attacked Iran nearly two weeks ago.

“They’ve violated but Israel’s violated it too,” Mr. Trump told reporters, referring to Iran and the cease-fire agreement as he boarded Marine One to begin a journey to The Hague for a NATO summit. Mr. Trump appeared to reserve greater criticism for Israel’s actions in the hours after the agreement was reached.

“Israel, as soon as we made the deal, they came out and they dropped a load of bombs, the likes of which I’ve never seen before. The biggest load that we’ve seen. I’m not happy with Israel,” he said, adding that he would be “really unhappy” if Israel attacked Iran on Tuesday in retaliation for what the president described as “one rocket that didn’t land.”

In a post on social media, Trump later warned Israel not to “DROP THOSE BOMBS,” saying “IF YOU DO IT IS A MAJOR VIOLATION. BRING YOUR PILOTS HOME NOW.”

Nearly two hours after Israel’s announcement confirming that it had agreed to the truce, sirens in northern Israel warned of missiles launched from Iran. Israel’s military accused Iran of breaking the cease-fire, saying in a statement that it would “respond with force.”

Israel retaliated by striking a radar system near Tehran, the office of Prime Minister Benjamin Netanyahu of Israel said in a statement released after Mr. Trump’s comments. Despite the threat to respond with force, the attack appeared to have been minor and symbolic.

In his comments to reporters, Mr. Trump also claimed that “Iran will never rebuild its nuclear,” apparently referring to the country’s nuclear program, which was one of the targets of Israel’s military campaign, along with Iran’s military leadership.

Mr. Trump said later that the cease-fire between Israel and Iran remained in effect.

“ISRAEL is not going to attack Iran. All planes will turn around and head home, while doing a friendly ‘Plane Wave’ to Iran,” Mr. Trump wrote on social media. “Nobody will be hurt, the Ceasefire is in effect! Thank you for your attention to this matter.” There was no immediate comment from Israel’s military.

President Trump announced on Monday evening — around 1:30 a.m. Tuesday in Tehran — that Iran and Israel had agreed to a cease-fire. Iran’s state television later announced a cease-fire early morning local time on Tuesday.

By then, Tehran residents had endured one more night of heavy attacks and terror.

Mariam, a 54-year-old art gallery owner, said in a tearful voice message that she and her teenage son were fleeing their home to her parents’ apartment because the airstrikes around them were too intense. Earlier on Monday, Israel’s military had urged people to evacuate their district, a densely populated residential and commercial area in central Tehran.

“I pray that when I return tomorrow I still have a house, they are flattening the city tonight,” Mariam said in the message. Like all the residents contacted for this article, she only provided her first name because of fear of retribution from the authorities.

Mostafa Shams, a journalist in Tehran, said the explosions around his house were loud and constant. He said he could see two jets flying over the area where he lives. As he spoke on Clubhouse, an audio-based social media platform, the audience of thousands could hear the boom and thuds of explosions.

Amir, a 48-year-old resident of Tehran’s Jordan neighborhood, shared a video that showed loud explosions and huge flashes of orange lighting up the night sky.

“No night has been like this, the sounds are huge, we can see fire and smoke from our window in multiple locations, We don’t know if we will be alive tomorrow morning,” said Alireza, a 27-year-old graduate student in Tehran, said in a phone message. He said he did not have electricity.

Residents of several other districts in Tehran also said that they did not have power. “It’s the most terrifying night we have experienced, we are sitting in darkness and hearing things blowing up,” said Roya, 60, who said she was huddling with her husband and daughter in the stairwell of her apartment building.

Ramin, who lives in Chitgar, a western suburb of Tehran, said many people in his neighborhood had come outside into the streets because they were afraid they might not survive the strikes if they stayed indoors.

“It feels like they are using much bigger bombs tonight,” he said at around 3 a.m. local time, describing his neighborhood as “shaking badly.” Reached by phone at around 6 a.m. after the cease-fire announcement on state television, Ramin said, “Is it really over? Thank God.”

Israel has accused Iran of violating the cease-fire and said it would retaliate. Iran’s military denied launching an attack after the cease-fire went into effect, Iranian state news outlets reported.

Here is what some leaders and governments have said:

United States: Mr. Trump, who helped broker the agreement, expressed displeasure with Israel and Iran on Tuesday, saying attacks appeared to have continued. “I’m gonna see if I can stop it,” he told reporters as he departed the White House to head to the NATO summit in the Netherlands.

Russia: Dmitri S. Peskov, the spokesman for President Vladimir V. Putin, said the Kremlin hoped the cease-fire would prove durable. “If a cease-fire has indeed been achieved, then that can only be welcomed,” he said. Russia and Iran are close allies, and Mr. Putin met with Iran’s foreign minister in Moscow on Monday, but there was no immediate indication that Russia had been involved in the diplomacy that led to the cease-fire announcements.

France: President Emmanuel Macron praised Mr. Trump’s announcement that a cease-fire had been agreed, but he said that “the situation remains volatile and unstable.” Speaking to reporters during a visit to Norway, Mr. Macron said: “The last minutes have shown that the situation remains very fragile.”

Germany: Chancellor Friedrich Merz said he welcomed Mr. Trump’s announcement and urged Israel and Iran to heed it. The United States and European countries would discuss ways to stabilize the situation later on Tuesday on the sidelines of the NATO summit, he said.

The Netherlands: Prime Minister Dick Schoof called the cease-fire a “good step to prevent further escalation in the region.” Iran must never become a nuclear-armed state, he said on social media, urging the country to return to nuclear negotiations.

Qatar: The cease-fire was in a “gray area,” Sheikh Mohammed bin Abdulrahman, prime minister of Qatar, told a news conference on Tuesday. “No party wants to be the party that was hit last,” he said. Qatar’s emir helped negotiate the cease-fire, he said, adding that “what we hope to see, truly, is a serious cease-fire, with the parties acting responsibly.”

Saudi Arabia: The country’s foreign ministry said in a statement that it welcomed the cease-fire announcement and valued “the efforts exerted to de-escalate tensions.”

European Union: Reports of missile fire underscore “just how fragile this cease-fire potentially remains,” Anouar El Anouni, an E.U. spokesman for foreign affairs, said during a news conference. “We do call on Iran to engage seriously in a credible diplomatic process,” he added.

The 12-day war began with a barrage of Israeli airstrikes on Iran that wiped out much of the Iranian military’s top brass, and destroyed its air defenses and some of its nuclear and missile facilities. Subsequent Israeli attacks killed hundreds of Iranians, including children. And American airstrikes on three Iranian nuclear sites damaged, or may have destroyed, key parts of the country’s nuclear program.

Still, Iranian officials were casting the outcome of the conflict as a resounding triumph for Iran and a decisive loss for Israel — a positive spin on what officials privately said was a face-saving effort to retaliate while avoiding an unwinnable all-out war with the United States.

In public, the tone was swaggering, emphasizing Iran’s response: first, Iranian missile barrages into Israeli towns that sent Israelis ducking into bomb shelters, destroyed buildings and killed 28 people; then, the missile strike on Monday on the installation in Qatar, Al Udeid Air Base, which left no casualties.

A retired Islamic Revolutionary Guards Corps naval commander, Gen. Hossein Alaei, told ISNA, a state news agency, that Iran had been able not only to withstand Israeli attacks but also to hit targets in Israel and then launch an attack of its own devastating enough to force the United States to retreat.

“In such circumstances, the warmongering Trump chose to accept a cease-fire and rein in the bloodthirsty Netanyahu,” he said, according to ISNA, referring to the American president and the Israeli prime minister, Benjamin Netanyahu.

Despite losing its top commanders, Iran proved it still had the capacity to strike Israel, General Alaei said. He added that the United States had entered the war only because “it became clear that Israel was unable to defeat Iran.”

Tehran had “forced the enemy to regret and accept defeat and unilaterally stop its aggression,” the statement from the Iranian national security council said. It praised the “dazzling power” of the military, adding that Iran’s attacks had proven that its forces “will be ready” to respond “to any act of aggression by the enemy.”

The government controls or restricts news outlets in Iran and has tightly limited internet access during the war, allowing little beyond its own message to filter into the country. Still, it is unclear how many Iranians — many of whom despise their theocratic leadership — will buy the official version of events. Although there has been widespread grumbling, mainly on social media, about the regime’s handling of Iran’s security, Iranians have also excoriated Israel and the United States for attacking their country.

On social media on Tuesday, some Iranians expressed hope that the fear and destruction would finally end, while others remained cautious, saying that it was not clear whether the cease-fire would hold. They also posted about their worries that the conflict would cause the government to crack down harder than ever on domestic critics. Only hard-line supporters of the regime were echoing its triumphal statements.

Security forces intercepted drones aimed at four other military sites operated by the Iraqi government, Mr. al-Numan added.

There were no immediate claims of responsibility.

The Taji base was a frequent target of rocket attacks by Iranian-linked Iraqi militias before U.S.-led coalition forces withdrew from the site in 2020. Once a major hub for American troops, the base was handed over to Iraqi forces that year as part of a broader drawdown by the United States in the country.

Iranian-linked militias have long played a dual role in Iraq as security enforcers and political power brokers, and have been implicated in past attacks on Iraqi and U.S. military bases.

Iraq’s prime minister, Mohammed Shia al-Sudani, ordered an investigation to identify the perpetrators and the circumstances surrounding the latest attacks, according to Mr. al-Numan.

The wave of drone attacks occurred just hours after Iran launched missiles at a U.S. military base in Qatar, an offensive that was telegraphed in advance by Tehran and was in response to American strikes on three nuclear sites in Iran. The tit-for-tat strikes marked a significant escalation after nearly two weeks of intense conflict between Iran and Israel.

On Tuesday, President Trump announced a cease-fire between Israel and Iran but the truce appeared to hang in the balance. The Israeli military said that Iran had broken the terms of the deal by firing missiles at Israel and vowed to retaliate.

The Iranian military denied firing missiles after the cease-fire went into effect, according to Iranian state news outlets.

Israel has accused Iran of violating the cease-fire and said it would retaliate. In a post on social media, Trump has warned Israel not to “DROP THOSE BOMBS,” saying “IF YOU DO IT IS A MAJOR VIOLATION. BRING YOUR PILOTS HOME NOW. DONALD TRUMP, PRESIDENT OF THE UNITED STATES.”

The attack in Beersheba, a city of about 600,000 in southern Israel occurred at around sunrise, not long after Mr. Trump said that a phased cease-fire had been agreed. But the official start time of the truce was unclear.

Hours after the strike, rescue workers were picking through the ruins of the building, advancing gingerly on ladders in a void where the middle three floors had been largely blown away. They were trying to access an area buried inside the structure where potential survivors may have been trapped.

One of the dead individuals was found inside the fortified safe room of an apartment and the three others were found outside of it, according to Col. Asher Benbenishti of the Israeli military’s southern home front command.

Two other buildings of a similar size in the complex, along with an adjacent school and nearby shops, also showed signs of serious damage. At the ground level, alongside a row of burned out cars, dozens of rescue workers had formed a human chain and were passing cement fragments from one to another to pile onto a growing mound of debris.

City welfare workers had set up a white tent outside the school building to process and gather information from residents of the ruined buildings, many of whom were still in pajamas and holding their phones. Russian-language translators in yellow vests were on hand to help residents who had immigrated to Israel from the former Soviet Union.

“I have only one question — where do I go now?” one resident, Timor Kovalev, 38, asked in English as he held his wife’s hand and pulled up a white plastic chair.

A city worker told them in Russian that they were being evacuated by bus to a hotel near the Dead Sea, to the north. Mr. Kovalev responded that he, his wife and two children needed to stay in Beersheba.

The direct missile hit was one of the deadliest single Iranian strikes since the war began in the early hours of June 13 with an Israeli military assault on Iran’s nuclear sites, military personnel and infrastructure.

The truce appeared tenuous, spurring anger from Mr. Trump.

About two hours after the Israeli government announced that it had agreed to the cease-fire, sirens wailed again in northern Israel. The Israeli military said it had identified more incoming missiles from Iran and threatened to retaliate forcefully for what it described as a “severe violation of the cease-fire carried out by the Iranian regime.” Iran’s military denied that it had fired any more missiles, according to Iranian state news outlets.

Israeli warplanes have pounded Iran since the start of the conflict, and Iran has fired more than 500 ballistic missiles and more than 1,000 drones, according to the Israeli government.

Iran’s attacks on Israel have killed 28 people, including those in Beersheba on Tuesday. Israeli attacks on Iran have killed 606 people and wounded 5,332 since the war began, according to Iran’s health ministry.

Images on Israeli television showed widespread destruction in a residential complex in Beersheba, a city in Israel’s Negev desert. Another missile struck a building in a major hospital complex in the city last week, causing serious damage, but no fatalities. Most patients and staff had already been evacuated or moved into other areas of the complex.

Israel has accused Iran of deliberately firing into civilian areas. Iranian authorities say the Israeli military has hit targets in civilian buildings in Iran, and caused many deaths.

Victoria Shifrin, who said she lived on the second floor of the building that was hit in Beersheba, told Israel’s Channel 12 television that she and her family had entered the safe room in their apartment when the sirens sounded. She said they heard a huge boom and the door of the fortified room blew in. “We understood it struck here,” she said.

Police and rescue services helped the family leave, Ms. Shifrin said. She said she left with nothing but the dress and slippers she had hurriedly put on and described climbing and half-sliding down a destroyed staircase. “I was shaking,” she said. “We were terrified.”

But the immediate consequences of the strike, at least for the direct conflict between the United States and Iran, appeared limited: President Trump said 13 of the 14 missiles Iran fired were downed and that there were no injuries or deaths among the roughly 10,000 American troops typically hosted there. A U.S. military spokesman said that the remaining missile had been allowed to land harmlessly. Satellite images captured by Planet Labs, a San Francisco-based Earth imaging company, showed that the base was nearly empty of aircraft ahead of the attack. Mr. Trump said the damage at the base was minimal.

Three Iranian officials said on Monday that their government had provided a warning about the strike to minimize potential casualties — allowing Iran a reprisal for the U.S. strikes on its nuclear sites while offering a way out of the direct conflict for both countries. Mr. Trump also said Iran had provided advance notice of the strike. “CONGRATULATIONS WORLD, IT’S TIME FOR PEACE!” he said on social media.

Similarly, Iran sent out an alert before retaliating in 2020 to the U.S. assassination of Iran’s most powerful security and intelligence commander, Maj. Gen. Qassim Suleimani, in a drone strike near Baghdad International Airport. It was a staggering blow for Iran and for Iranians, many of whom regarded him as a national hero. The country’s supreme leader, Ayatollah Ali Khamenei vowed a “forceful revenge.”

But days later, when Iran fired a series of ballistic missiles at American troops in Iraq, it gave the Iraqi government notice of the impending attack. The office of Iraq’s prime minister at the time, Adel Abdul Mahdi, said in a statement that it had received “an official verbal message” from Iran that its retaliation for the killing of General Suleimani had begun or would begin shortly and would be limited to sites where American troops were present.

The Pentagon said more than two dozen missiles were fired at two military bases in Iraq where American troops were stationed, Al-Asad and Erbil. Shortly after those strikes, both sides appeared to stand down. Iran’s foreign minister, Mohammad Javad Zarif, said on social media that Iran had “concluded proportionate measures in self-defense” and that his country did “not seek escalation or war, but will defend ourselves against any aggression.”

As in Iran’s attack on Al Udeid on Monday, Mr. Trump suggested in 2020 that initial assessments had found minimal damage and few casualties sustained by American forces. The Defense Department later said that more than 100 American service members had sustained traumatic brain injuries from the Iranian strikes on Al-Asad Air Base but that most had returned to duty.

Eric Schmitt and Farnaz Fassihi contributed reporting.

The announcement, made minutes after 6 p.m. Eastern time, caught even some of Mr. Trump’s own top administration officials by surprise. But within three hours of Mr. Trump’s announcement, there were fresh attacks from Israel against Iran.

Mr. Trump had help in pressing for a cease-fire from Vice President JD Vance, Secretary of State Marco Rubio and Steve Witkoff, Mr. Trump’s special envoy, who had been leading the efforts over the last two months for a deal to curtail Iran’s nuclear program, the official said.

The three men worked through “direct and indirect” channels to reach the Iranians, the official said. Israel agreed to the cease-fire provided they aren’t subject to further attacks from Iran, the official said.

The official credited the U.S. military strikes on three Iranian nuclear enrichment sites on Saturday with setting the conditions for a cease-fire discussion.

The official did not say what conditions Iran may have agreed to, including whether it answered questions about the whereabouts of its stockpile of enriched uranium.