The strikes came hours after Mr. Trump assailed Iran’s leaders as “evil” and “scum” during the NATO summit in Turkey. “I think it’s over,” he said of the cease-fire, although he said that he was still open to negotiations and that he did not expect a return to all-out war. Any military action, he said, would “go very quickly.”

Mohsen Rezaei, a senior military adviser to Iran’s supreme leader, issued a warning early Thursday morning after the U.S. strikes. “The aggressor enemy and its accomplices will be severely punished,” he wrote on social media,

The temporary truce has appeared tenuous almost from the moment it was signed last month, and the latest flurry of strikes seemed to have it on the verge of collapse. Each side has repeatedly accused the other of violating the terms of the cease-fire.

The latest violence centered on the Strait of Hormuz. Iran has asserted that the terms of the deal give Tehran oversight of the economically vital waterway, and it has demanded that vessels use Iran’s preferred routes through it. The United States has accused Iran of repeatedly targeting ships in the strait, although Tehran has not claimed responsibility for a series of strikes in recent weeks.

The strikes that began just before midnight in Tehran were the second in two days by the United States in response to attacks on three commercial vessels in the strait this week. On Tuesday, the United States revoked a sanctions waiver on Iran’s oil industry — a provision of the cease-fire that had been a major victory for Iran — and soon after attacked Iranian military targets.

In response, Iran’s armed forces said that they had attacked American military sites in Bahrain and Kuwait earlier Wednesday, although no major damage was reported.

Shipping traffic in the Strait of Hormuz has once more come to a halt, driving oil prices to their highest levels in two weeks.

The temporary truce was intended to reopen the strait and halt the fighting, but left some of the thorniest issues, particularly Iran’s stockpile of highly enriched uranium and the future of its nuclear program, to be sorted out during a 60-day negotiation period.

On Wednesday, however, Iranian media outlets close to the country’s powerful Islamic Revolutionary Guards Corps published editorials calling for “the official end” to the deal.

As the multiday funeral services continued for Ayatollah Ali Khamenei, the Iranian supreme leader killed on the first day of the war, Mr. Trump boasted that all of Iran’s leaders were “gone,” before adding that he was himself “No. 1 on the kill list for Iran.” A social media account belonging to the supreme leader’s successor, his son, Mojtaba Khamenei, posted a doctored image depicting a snake emanating from Mr. Trump’s signature on the cease-fire deal.

Here’s what else to know:

• Energy prices: Oil prices, which had fallen back near prewar levels following the cease-fire deal, rose 5 percent to about $78 a barrel. That is down from its peak during the worst of the fighting but above its prewar price of around $72 a barrel. Read more ›

• Strait of Hormuz: The uptick in violence is threatening to derail the fragile recovery of oil and gas shipments through the crucial waterway. On Wednesday, the head of the International Maritime Organization urged ship operators to avoid sending vessels through the strait.

• Khamenei’s funeral: Talks between the United States and Iran had been paused during funeral ceremonies for Ayatollah Khamenei. The supreme leader’s body was taken on Wednesday to Najaf, a holy Shiite city in Iraq. Read more ›

In a statement, Steven Cheung, the White House communications director, said that “the new Air Force One is a state-of-the-art aircraft that has been fitted with high-level security protocols that ensure the safety of the president and his staff.”

“As the president has said recently, there are many enemies of America who have their sights on him, and we use every tool at our disposal — including distraction and misdirection — to address those threats,” he added.

But people briefed on the new plane’s capabilities, who spoke on the condition of anonymity to discuss sensitive security issues, said the new plane does not have all the features of the older plane. The switch in the president’s aircraft when he departed Turkey was a precautionary measure made at the advice of the Secret Service and not because of a specific threat, they said.

Mr. Trump, who has marveled at the luxury touches of his new jet, flew on it on Monday night to go to Turkey for a NATO summit. After his arrival, the conflict with Iran reignited, and the United States launched a series of strikes against that country while Mr. Trump and NATO leaders were about 1,000 miles away in Ankara.

The president on Wednesday denied that the change in his aircraft was made because of security concerns. Instead, he asserted that the swap was so the new jet could leave early and make stops at U.S. military bases to show it off to the troops because the aircraft is “magnificent.”

But when pressed by reporters in Ankara about the reason for the change, Mr. Trump also repeatedly noted that he was Iran’s No. 1 target, and referred at one point to having seen or been briefed on a list of Tehran’s targets in recent days.

Earlier Wednesday, Mr. Trump wrote in a social media post that he would fly aboard the older aircraft “for old time’s sake” out of Ankara so that the newer plane could be shown off at Mildenhall Air Force Base in England to give U.S. troops a “chance to tour the Aircraft.”

The Secret Service declined to comment, referring to the president’s post as the explanation for the change.

When Mr. Trump departed Ankara, he boarded the old aircraft unusually quickly, before the journalists traveling with him could watch or photograph him ascending the steps, as they typically do. Passengers on board were also instructed to pull their window shades down before takeoff.

The plane landed at Mildenhall late Wednesday night, and then the president switched to the new jet to return to Washington.

After Mr. Trump departed, he told reporters that they had probably been instructed to close their blinds when leaving Ankara because they were “on a dangerous plane” due to the threat from Iran.

The older plane has been widely reported to be equipped with a system designed to blind an incoming antiaircraft missile, along with “chaff” that could be deployed to mislead a missile and force it off course.

It is unclear how many, if any, of those capabilities have been installed on the newer plane that was donated from Qatar, which Mr. Trump has been eager to get into service.

Industry and Pentagon officials have said such an extensive upgrade could cost as much as $1 billion and take up to two years to complete. But in testimony before Congress, Troy E. Meink, the Air Force secretary, estimated that the modifications would run “probably less than $400 million.”

The Air Force started upgrading the 747 jetliner in the United States last summer.

Air Force officials said at the time that they were modifying the jet for “executive airlift” support, on orders of Defense Secretary Pete Hegseth, but that all other details about the upgrade were classified.

The plan immediately drew criticism from some members of Congress. The lawmakers expressed concern that Mr. Trump would pressure the Air Force to do the work so fast that sufficient security measures would not be built into the plane, including missile defense systems or even systems to protect it from the electromagnetic effects of a nuclear blast.

Much of the retrofitting and refurbishing that the Air Force described took place at a Texas facility known for secret technology projects.

Andrew P. Hunter, the former Air Force assistant secretary who was in charge of the Air Force One program during the Biden administration, said that a true retrofit of a 747 jet to prepare it to become Air Force One would require more than a year of work.

That is because the base plane, even if it has a luxurious interior, needs significant modifications to its physical structure to accommodate special security upgrades — work that would have taken longer than the Air Force had to retrofit the donated Qatari jet.

Mr. Hunter would not name the more complicated security upgrades individually because they are considered classified. But other government officials have told The New York Times that this more complex work includes advanced missile defense systems and hardening of the plane’s wiring to protect it from an electromagnetic pulse, in case there is a nuclear strike. It is unclear whether such work was done to the Qatari jet.

“In that time they had, they would be able to accommodate communications upgrades,” Mr. Hunter said, referring to vital security equipment that allows a president to be in contact at all times. “But not anything that would require significant structural work.”

Mr. Hunter added: “To do a full Air Force One equivalent upgrade does require structural modifications.”

The Times asked the Air Force earlier this year whether these kinds of measures had been included in the updates to the Qatari jet. The Air Force declined to respond to the questions.

Doug Mills and David E. Sanger contributed reporting.

The latest strikes, the U.S. Central Command said, were intended to undermine Iran’s ability to threaten ships in the Strait of Hormuz, a critical waterway for global energy supplies that has become a central issue in the conflict.

Central Command called the attacks retaliation for “recent unjustified aggression against commercial shipping and civilian crews.”

Mr. Trump said earlier on Wednesday that while the United States would probably hit Iran “hard,” he did not expect a return to all-out war. “I don’t think it’s going to start again,” he told reporters at a NATO summit in Turkey. “I think it’s going to go very quickly.”

But later in the day, he said in a social media post that if Iran attacked ships again, “it will get much worse!”

Speaking aboard Air Force One while on his way back to the United States from the summit, the president maintained that Iran still wanted to make a deal despite the renewed and intense hostilities.

“They called a little while ago. They want to make a deal so badly,” he said. “I just don’t know if they’re worthy of making a deal. I don’t know that they’re going to honor the deal.”

The Iranians have said nothing about new negotiations.

Even before the strikes, the temporary truce in the four-month conflict between the United States and Iran had appeared on the brink of collapse, with each side accusing the other of repeatedly violating the terms of the agreement.

On Tuesday, the United States carried out airstrikes against more than 80 targets in Iran in retaliation for what the Pentagon said were Iranian strikes against three commercial ships, including a Saudi oil tanker and a Qatari vessel carrying liquefied natural gas.

The American strikes — about seven times the number the U.S. military launched in the round of retaliatory strikes in late June — targeted Iranian air defense systems, command and control networks, coastal radar sites, anti-ship missile capabilities and more than 60 Islamic Revolutionary Guards Corps small boats, Central Command said.

The strikes on Tuesday came hours after the Trump administration revoked a waiver allowing the sale of Iranian oil around the world.

Tehran has not claimed responsibility for the ship attacks. After the U.S. strikes and re-imposition of sanctions on oil sales, Iranian officials announced in a series of statements that the United States had violated the June 18 agreement intended to end the war.

Negotiations between Iran and the United States have been paused until after the multiday funeral ceremonies for Ayatollah Ali Khamenei, the supreme leader who was killed on the first day of the war.

Although the United States and Iran have agreed to restore access to the strait — with Mr. Trump declaring the waterway open to unrestricted navigation — the preliminary accord does not stipulate exactly how that should happen, and assigns to Iran the task of allowing the long-blocked traffic to get through. Iran has insisted that commercial ships sail near its shore, in a channel under Iran’s control, but many vessels are using American help to take a route near the Omani coast.

“What we’re seeing now is Iran, and more specifically the I.R.G.C., trying to exert control over the strait and declaring that this control is their sovereign right,” said Kevin Donegan, a retired Navy vice admiral who is a former top Navy commander in the Middle East.

“That’s the main card they have to play, and as a result we can expect they will continue to try to disrupt any ship traffic that uses routes different from the ones they have published,” Admiral Donegan said.

Erica L. Green contributed reporting.

The faction that favors talks has at the same time accused the United States of violating the terms of the truce agreement. These officials include President Masoud Pezeshkian, who on Wednesday said Washington was “bullying rivals, creating obstacles and cheating.”

The rival group, drawn from a minority of hard-liners, has directed its anger at the Iranian president and negotiating team.

The rising tensions inside and outside of Iran have unfolded against the backdrop of Iran’s weeklong funeral for its slain supreme leader, Ayatollah Ali Khamenei, with ceremonies taking place in five cities in Iran and Iraq. Mr. Khamenei’s body had reached Najaf, Iraq, when the American airstrikes began and was scheduled to return to Iran for burial in Mashhad on Thursday.

All week, as the funeral has progressed, the hard-line faction in Iran has targeted government officials.

Mr. Pezeshkian was attacked on Monday by a crowd of hard-line supporters, who tried to tackle him while shouting “death to the appeaser,” as he attended the funeral procession, according to videos on social media and shared by his office. Mr. Pezeshkian swayed, looking dazed, as his security detail dragged him and pushed away the crowd.

Another government official in his camp, Foreign Minister Abbas Araghchi, was assaulted with a rock on Monday as he was chased down an alley during the funeral. His attackers, waving flags, cursed him and called for his death, video of the incident posted on social media showed.

Government officials and supporters called for the arrest of the people who attacked the president and foreign minister, and urged the judiciary to hold the hard-liners accountable.

Not long after those incidents, hostilities over the Strait of Hormuz had begun again. Iran’s Islamic Revolutionary Guards Corps targeted several commercial ships passing through the critical waterway this week. Early Wednesday, the United States carried out intense airstrikes on dozens of targets along Iran’s southern shores. Iran retaliated by launching ballistic missiles and drones targeting American military bases in Kuwait and Bahrain.

By Wednesday night, the United States was striking Iran again. Two senior Iranian officials, with knowledge of internal leadership deliberations, described the situation inside Iran’s political circles as being in disarray. The officials spoke on the condition of anonymity because they were not authorized to discuss government security matters. They said no decision has been made about how to proceed — whether to resume conflict or continue diplomatic engagement — and that a blame game was in full swing within Iran.

But the officials said Iran would retaliate forcefully to new attacks, echoing statements made this week by the Revolutionary Guards.

“What shall be done in response to someone who has no commitment to their own word or signature?,” Mehdi Tabatabaie, the deputy communication chief for the president’s office, asked on social media on Wednesday, in an apparent reference to Mr. Trump’s comments about the cease-fire.

Yousef Pezeshkian, the son and adviser of the president, wrote a long defense of the policy of engagement with the United States on social media. He condemned the attacks on his father and other officials by hard-liners. “If this anger is directed at our own officials and targets domestic unity and larger Islamic unity, it means it has become a tool for the enemy,” he said.

Now Mr. Trump appears to be confronting the consequences of his haste, and of his assumption, born of his time in the real estate business, that his adversary would prize economic benefits over the revolutionary ideology that has driven its politics since the 1979 Iranian revolution. That has left him facing a range of unpalatable options amid seemingly intractable sticking points over the fate of Iran’s nuclear program — to say nothing of its missile program, its support for terrorist groups and its repression of its own people.

At the NATO summit in Ankara, Turkey, on Wednesday after the two sides had exchanged strikes, he threatened major new combat operations. Those included seizing a key Iranian oil processing island and attacking the country’s infrastructure and desalination plants, which experts have said could constitute a war crime. (Mr. Trump did say he was most hesitant to hit the desalination facilities.)

But Mr. Trump has made such threats without following through before, and he added on Wednesday that he did not anticipate a return to full-scale war. Such a move has little domestic support, and some of Mr. Trump’s Republican allies fear the economic and political consequences less than four months before the midterm elections. No one is more aware of that calendar, or Mr. Trump’s hesitation to repeat the experience of the spring, than the Iranian leadership.

The president could instead reimpose the American blockade of Iranian ports, an attempt to cut off the country’s economic lifeline. But that would require a continued, intense American presence in the region, and while Mr. Trump contended in April that it would lead to Iranian economic collapse, his earlier imposition of it did not.

Or he could elect to live in a world of neither war nor peace, an era of episodic skirmishes in the Persian Gulf, punctuated by periodic negotiations, with traffic through the Strait of Hormuz, a key oil-shipping route, greatly reduced from the 130 or so ships that passed through each day before the war. The energy markets would most likely adjust; to some degree they already have.

But for a president who promised a quick, cost-free confrontation with an old adversary — “four to six weeks” was the White House prediction in the opening weeks — an ongoing conflict would amount to near-total failure on the mission he initially set out upon. And the price would be staggering: The Pentagon has already asked Congress for about $70 billion to cover the early operations around Iran, and the cost rises every week.

“The problem is that all the options — endure, escalate or agree — are unattractive in different ways,” Richard Fontaine, the chief executive of the Center for a New American Security and a former aide to Senator John McCain, said on Wednesday. “The likeliest outcome is a continuing series of low-level, tit-for-tat attacks, followed by frantic diplomacy by mediators, the emergence of a new and fragile cease-fire, and then probably another round of strikes.

Mr. Fontaine added: “It will be a long oscillation between cold war and low-level hot war.”

Many of the problems Mr. Trump is facing today were exacerbated by the cease-fire deal itself. It left unresolved, for a later negotiation that Mr. Trump now says he has little interest in pursuing, the fate of Iran’s stockpile of near-bomb-grade nuclear fuel, the most prominent among the administration’s shifting reasons for attacking Iran on Feb. 28.

The agreement appeared to hand Iran at least some control over passage through the Strait of Hormuz, the superweapon that Tehran, and specifically the Islamic Revolutionary Guards Corps, has skillfully manipulated to drive up oil prices, and now has used to justify attacks on tankers and cargo ships not hewing to its new rules.

“What we’re seeing now is Iran, and more specifically the I.R.G.C., trying to exert control over the strait and declaring that this control is their sovereign right,” said Kevin Donegan, a retired Navy vice admiral who served as a Navy commander in the Middle East. “That’s the main card they have to play, and as a result we can expect they will continue to try to disrupt any ship traffic that uses routes different from the ones they have published.”

The deal was silent on Iran’s missile arsenal, the key issue for Israel. And it depended on a cease-fire in Lebanon, though the parties to that conflict, Israel and Hezbollah, were not signatories of the agreement. And it set an unrealistic deadline, 60 days, to deal diplomatically with those and other issues that months of active combat had failed to resolve.

There are, of course, many more turns ahead in this drama. Mr. Trump threatened again on Wednesday to try to seize Kharg Island, where giant tankers collect Iran’s oil and head to world markets. He may seek to seize the 60 percent enriched nuclear material deep underground at Isfahan, a mission for which Special Operations forces have trained extensively, though he dismissed the need for it on Wednesday.

“We’ve already got the nuclear material, because it’s so far underground,” he said, noting that the Iranians do not have the heavy equipment needed to unearth it.

If Mr. Trump is right about that, and many nuclear experts agree that the material would be enormously difficult to recover, it raises a fundamental question: If the nuclear fuel was successfully buried in the June 2025 American bombing of three major nuclear sites, why did he go to war to begin with? His statement on Wednesday, a repeat of comments he has made several times in recent months, undercuts the argument he made in the days after the initial attack in February that there was an “imminent” threat.

That initial justification has been overtaken by subsequent contradictions. Mr. Trump has periodically praised the new Iranian leadership, and even its new supreme leader, Mojtaba Khamenei, the son of the slain ayatollah, as more “reasonable.” He has said many times that, unlike their predecessors, the new leaders would open up the strait and dilute the nuclear stockpile because it will be in their economic interest.

Vice President JD Vance sounded exactly that note last month, when he was signing the memorandum of understanding in Switzerland.

“The coolest thing about the progress we’ve made over the last few weeks is that you see people within the Iranian system, senior leadership, even I.R.G.C. officials say, ‘You know what, we may have some animosity, we may have some mistrust, but we recognize the way that we’ve done business with the United States for 47 years is a mistake,’” he said.

On Wednesday, Mr. Trump had a different word for those leaders: “scum.”

“They are sick people. They’re led by sick people, and they’re vicious, violent people,” he said, adding: “As far as I’m concerned, it’s just a waste of time dealing with them.”

Eric Schmitt contributed reporting.

By midday Wednesday, international oil prices were approaching $80 a barrel, their highest level in weeks, after President Trump said the temporary truce with Iran was “over.”

Oil is trading at prices that have been fairly typical in recent years. But the international benchmark, Brent, has risen sharply from the start of the week when it was below prewar levels and analysts were warning that the world might soon face a glut.

“The honeymoon phase is over,” said Dan Pickering, chief investment officer for Pickering Energy Partners, a financial services firm based in Houston. “We’re being reminded that this is still an active conflict.”

The latest flare-up was set off by Iran’s efforts to exert more control over the Strait of Hormuz by striking vessels that were not following the country’s preferred route through the waterway. The United States responded by attacking Iran and revoking the sanctions relief it had provided for the country’s oil industry.

Iran then targeted U.S. military sites in Bahrain and Kuwait, and its foreign ministry said recent U.S. actions had rendered ineffective “important and essential parts” of the deal between the countries.

The United States would probably launch more strikes against Iran on Wednesday night, Mr. Trump said in Ankara, Turkey, where he was attending a NATO summit. He also floated the possibility of reinstating a blockade on vessels traveling to and from Iranian ports.

Analysts nevertheless remained optimistic that oil would not soon return to wartime highs, partly because millions of barrels of oil have been shipped out of the Persian Gulf in recent weeks. In addition, the United States and Iran previously agreed to continue negotiating after engaging in hostilities, said Kevin Book, managing director of ClearView Energy Partners, a Washington-based research firm.

“We had skirmishes at the end of June that didn’t really stop traffic,” Mr. Book said.

Still, this week’s attacks and counterattacks are a reminder that resolving the conflict between the United States and Iran — and allowing ships to regularly pass through the Strait of Hormuz without incident — will be anything but a smooth process. Given that uncertainty, oil prices may not fall to very low levels.

The war with Iran is the latest in a succession of crises that provoked energy shocks, including the Covid-19 pandemic, Russia’s invasion of Ukraine and Mr. Trump’s “Liberation Day” tariffs.

“Until something very different changes, prepare for more volatility,” said Tyler Rosenlicht, head of natural resource equities at Cohen & Steers, an investment firm.

In the short term, some of the biggest questions facing the oil market include whether Mr. Trump re-establishes the blockade on Iran and how shipping companies react to the heightened conflict. The head of the International Maritime Organization told shipowners on Wednesday to avoid the strait to protect seafarers from “unnecessary danger.”

Iran, which spent the early weeks of the war attacking energy facilities in Gulf countries, has refrained from doing so recently, even as tensions have flared with the United States. Oil prices would probably climb much higher if that changed.

Neil Quilliam, an expert on the Gulf states at Chatham House, a London-based research organization, said he believed more U.S. strikes would prompt Tehran to target U.S. bases and energy infrastructure throughout the Gulf. One thing Iran won’t do, he said, is cede control over the Strait of Hormuz.

“They have found they can exercise control over Hormuz, and this was relatively new to them and it’s not something they want to give up,” he said. “They would be willing to suffer the dire economic consequences of the U.S. imposing the blockade again as long as they can hold on to exercising some kind of control over Hormuz.”

The other big wild card is China, which has helped stabilize global energy markets by sharply reducing oil imports during the war. If it continues to hold back purchases, that will keep a lid on oil prices. The reverse is also true.

“They’re absolutely managing price and volatility very well,” Mr. Pickering said of China. “You can’t do that forever.”

The attacks were an escalation after weeks of occasional exchanges of fire despite a nominal truce that Iran and the United States signed last month.

U.S. officials hoped the cease-fire would fully reopen the Strait of Hormuz, the vital waterway that Iran blockaded after the war began in February. But ships in the strait have come under fire in attacks widely blamed on Iran, prompting U.S. retaliation. Iran has then responded by attacking American installations in the Persian Gulf, eroding hopes for a speedy return to normal life there.

Before Iran’s strikes on Wednesday, U.S. forces attacked Iran overnight, hitting dozens of sites. Iranian state media reported that at least eight Iranian forces had been killed in the attack, which U.S. officials said was a response to the bombardment of three commercial ships in the Strait of Hormuz this week.

Iran has not claimed responsibility for attacking ships, and its military condemned the U.S. strikes as an “overt act of aggression,” vowing “a crushing response.”

Hours later, Iran’s Islamic Revolutionary Guards Corps said that it had targeted 85 U.S. military sites in Bahrain and Kuwait. In a statement carried by Iranian state television, the Revolutionary Guards claimed to have attacked the Ali Al Salem Air Base in Kuwait, as well as the U.S. Fifth Fleet’s naval base and Khalifa Bin Salman Port in Bahrain.

The Iranian military also shot down an American MQ-9 drone, the Guards said. The U.S. military did not comment on the Iranian claim.

The Kuwaiti government said at least two ballistic missiles and 13 drones had been fired at its territory, all of which were intercepted. There were no reports of casualties, although Kuwait’s energy ministry said some power lines had been damaged by falling shrapnel.

In Bahrain, air-raid sirens sounded throughout the morning. The country’s military said it had intercepted Iranian missile and drone attacks, without specifying whether there had been any damage.

“He was our guardian and protector, and we are here today to return the favor,” said Rabab Jassim, a 45-year old homemaker, who arrived in Najaf at 3 a.m. from Baghdad to join the ceremony. “My heart is on fire,” she said, bursting into tears.

The procession followed five days of funeral services and mass mourning inside Iran for Ayatollah Khamenei, who was killed in the first U.S.-Israeli strikes that launched the war on Iran in February. His body was set to be flown back to Iran after the commemorations, and he was expected to be buried on Thursday in his hometown, the northeastern city of Mashhad.

As supreme leader, Ayatollah Khamenei oversaw brutal crackdowns of opposition to his clerical rule at home, and he also leaves behind a divisive legacy in Iraq.

The country is home to the Middle East’s second-largest Shiite Muslim population, after Iran. Some Iraqis praise Ayatollah Khamenei for providing Iranian support to Iraq’s Shiite militias, who fought against the eight-year U.S. occupation. Others blame Iran’s intervention for stoking two decades of sectarian bloodshed with Iraq’s Sunni minority that has only recently ebbed.

People from all over Iraq have spent days awaiting the commemorations in Najaf and Karbala, home to two of Shiite Islam’s holiest sites.

Some came from even farther afield: Among the crowds were Nigerian women, holding up their babies; Lebanese mourners draped in the yellow flag of the Iranian-backed militant group, Hezbollah; and Yemenis wearing traditional scarves and daggers.

“I chose to come here, instead of Iran, because this is a much more powerful religious experience, standing at our holiest sites,” Samir Rabyani, a medic from Sanaa, Yemen, said. “Khamenei died a martyr. And no matter how many of us they martyr, we will be the victors.”

The crowds, drenched in sweat after walking for hours in searing temperatures, turned into a crush as mourners tried to follow the coffin into Najaf’s golden-domed Imam Ali shrine. They trampled soldiers to force their way inside, and mourners who fainted had to be carried out on others’ shoulders.

There is little historic precedent for one country holding an official funeral for the leader of another nation, as Iraq’s top officials did on Tuesday evening, when the ayatollah’s coffin arrived in the country. That makes the event as unusual as it is symbolically potent.

“Iraq is the holy land of the Shiite faith, and this is an attempt by Iran to underscore Khamenei as belonging not just to Iran, but to the broader Shiite community,” said Arash Azizi, a New York-based historian and author of several books on Iran.

It was also a political message, projecting the reach that Iran and its allies claim still to have.

For the past three years, the United States and Israel have sought to dismantle the network of mostly Shiite militant groups that Iran cultivated during Ayatollah Khamenei’s nearly 37-year rule.

Among those groups is Hezbollah in Lebanon, which Israel has been at war with, and the Houthi militants in Yemen, against whom the Trump administration fought a short-lived campaign. Since June 2025, the United States and Israel have also started two wars on Iran itself, battering but failing to topple the country’s Shiite theocracy.

In Iraq, Tehran maintains its alliances with many Shiite militias, and the funeral is a sign that those bonds are far from broken. Iran’s resilience in the recent war even emboldened those militias enough to hold a procession for Ayatollah Khamenei in Iraq — a regional ally of the United States.

“The message here is that we defied the world: America, Israel, and the great global powers,” said Ali Ramadan, a fighter in an Iraqi Shiite militia who had brought his family of four to Najaf for the funeral.

Video

Funeral-goers trying to keep cool.

“We are with justice, and we are with Iran,” Mr. Ramadan added. “Khamenei stood for truth against imperialism.”

The ayatollah’s coffin, draped in an Iranian flag and encased in glass, was escorted by a procession of trucks emblazoned with the words, “By god, rise up.” By evening in Karbala, so many people had packed the streets that the procession had slowed to a crawl on its way to the Imam Hussein and al-Abbas shrines, festooned with strings of glowing red lights.

“No one can humiliate us,” the mourners chanted in unison, while a speaker at the procession shouted, “We take pride in our tears as we mourn your coffin.”

Thousands of Iraqis camped out overnight in the streets of Najaf and Karbala to await the processions — enduring temperatures that topped 90 degrees before sunrise.

Some had pictures of Ayatollah Khamenei pinned to their chests, while others waved Iranian and Iraqi flags. Iraqi tribesmen chanted and danced their way through the crowds. Older participants hobbled up to the procession routes with canes, as militia fighters sprawled out in the shade below bridges.

Iranian and Iraqi officials have made the funeral in Iraq an exercise in modern-day mythmaking, repeatedly comparing Ayatollah Khamenei to figures in Shiite Islam’s most sacred stories.

Along the procession routes in Karbala, Ayatollah Khamenei’s face was emblazoned on black-and-red banners commemorating Hussein, the Prophet Muhammad’s grandson. Hussein’s martyrdom in the 680 A.D. battle of Karbala is a central theme of Shiite Islam, representing the willingness to fight tyranny in the face of certain death.

Iranian officials and Iraqi mourners have likened Ayatollah Khamenei to a modern-day Hussein, and the United States and Israel to the story’s tyrant.

“He fought for justice. And what happened to him is what happened to Hussein,” said Abbas Jassim, a 26-year old security guard, who had tied an Iranian flag around his shoulders like a cape. He was so eager to reach the funeral in Karbala, he said, he sold his daughter’s earrings to afford the bus fare from Baghdad.

“I would now sacrifice my soul for Iran,” he said. “And I reached that point because of my love for Ali Khamenei.”

Many Iraqi Shiites, remember Ayatollah Khamenei most for being the first leader who sent weapons and support to help Iraq fight back against the jihadist forces of the Islamic State, or ISIS, in 2014. The Islamic State, a Sunni militant group, seized swaths of Iraq, slaughtering many Shiites as they advanced.

Most mourners said that stood foremost in their minds when they decided to attend the commemorations for Ayatollah Khamenei.

“I lost a dear friend to ISIS, and that was like losing the ribs that protect your heart,” said Ibrahim Enad, a 30-year-old engineer, tearing up. “We cannot forget the Iranian stance toward Iraq. In all of our crises, they have never abandoned us.”

Falih Hassan and Shirin Hakim contributed reporting.

As a team from The New York Times prepared to board a flight from the capital, Tehran, to Mashhad, Iran announced that its armed forces had targeted 85 American military sites in the Persian Gulf states of Bahrain and Kuwait, further imperiling the U.S.-Iran cease-fire.

In Mashhad, however, the focus was elsewhere.

At the arrivals terminal of the city’s airport, posters and banners bearing Ayatollah Khamenei’s image lined the entrance, some emblazoned with the slogan, “We Must Rise.” Two large screens displayed an A.I.-generated animation of the former supreme leader walking.

Volunteers greeted arriving passengers with walnut cakes, welcoming the crowds ahead of Thursday’s burial, the final moment after a week of elaborate funeral ceremonies attended by millions of people.

Nearby, another display drew the attention of passengers. Dozens of mostly pink and blue backpacks had been arranged in memory of children killed when an elementary school in the southern town of Minab was struck early in the war. At least 175 people, most of them children, were killed, according to Iranian officials.

Privately, U.S. military officials have acknowledged American forces carried out the strikes that hit the school and cast them as an intelligence failure.

In the terminal, each backpack was paired with a rose and a pair of children’s shoes. Behind them, a screen cycled through images of destruction in Iran, Lebanon and Gaza. Visitors stopped to photograph the memorial, while others collected pins commemorating those killed in the attack.

Together, the displays illustrated Iran’s command of political symbolism, using imagery, ceremony and carefully choreographed public spaces to project resilience and authority. That message has taken on added importance for both foreign and domestic audiences after Ayatollah Khamenei was killed in late February in the opening attacks of the U.S.-Israeli war.

Across Iran, funeral ceremonies have unfolded over several days, including funeral prayers at the Grand Mosalla in Tehran, a procession through Azadi Square and prayers at Qom, the center of Shiite religious education in Iran. On Wednesday, prayers were also being held in neighboring Iraq before Ayatollah Khamenei’s body was to be flown to Mashhad for burial at the shrine of Imam Reza.

By midmorning on Wednesday, crowds carrying Iranian flags had already begun gathering along Imam Reza Boulevard leading to the shrine. The thoroughfare was decked with banners and posters bearing Ayatollah Khamenei’s face, along with red flags calling for his death to be avenged. Security forces lined the streets from the airport into the city.

The Trump administration launched a series of strikes on Iran and revoked a waiver that had allowed Iran to sell oil. The actions against Iran on Tuesday were in retaliation for attacks on tankers this week in the Strait of Hormuz, a crucial conduit for the world’s energy.

U.S. Central Command said that it hit over 80 targets in Iran, including dozens of small boats used by the Iranian military, “to degrade Iran’s ability to continue attacking international commerce.” Iran’s military responded by targeting 85 U.S. military sites in Bahrain and Kuwait, prolonging a retaliatory cycle that could impede the nascent recovery in shipping traffic in the region.

Oil prices rise sharply, breaking a relative period of calm.

• Brent crude oil, the international benchmark, rose more than 5 percent, to around $78 a barrel when prices settled on Wednesday, its highest level in over two weeks. Although down significantly from its peak during the worst of the fighting, the recent jump pushed oil back above its prewar price of around $72 a barrel, where it had hovered for several days.

• West Texas Intermediate crude, the U.S. benchmark, also jumped, to more than $73 a barrel. This grade of crude traded at $67 per barrel before the war.

• Daniela Hathorn, an analyst at Capital.com, a broker, said that investors had viewed the cease-fire as “fragile but ultimately durable,” until Mr. Trump’s comments on Wednesday called that into question. “Any suggestion that negotiations have collapsed raises the risk of renewed supply interruptions or tighter sanctions,” Ms. Hathorn said in a statement.

• Gasoline prices don’t move in lock step with crude. The U.S. national average price of gas was $3.80 a gallon on Wednesday, according to the AAA motor club. That price remains more than 27 percent higher than it was at the eve of the war in late February, amid signs that gas stations are maintaining wider profit margins amid the volatility.

A tentative recovery in shipping appears at risk.

• The attacks on Tuesday on three commercial vessels, including a Saudi oil tanker and a Qatari liquefied natural gas carrier in the waters around the Strait of Hormuz, threatened to throttle the flow of energy. Ship traffic through the strait had recovered somewhat as shipowners gained more confidence in sending vessels through the contested waterway.

• The Joint Maritime Information Center, a multinational organization that assesses threats on high-risk shipping routes, said on Tuesday that the risk of sending ships through the strait was “severe,” up from “substantial,” with further “hostile action considered likely under current conditions.”

• On Tuesday, 41 ships passed through the strait in both directions, according to Kpler, a maritime data company. Before the war, more than 130 ships a day routinely passed through the choke point between Iran and Oman. Many of the vessels that went through the strait this week used the Iranian corridor, which the Iranian authorities, trying to assert more control over the waterway, have said is the only viable route.

• Arsenio Dominguez, secretary-general of the International Maritime Organization, on Wednesday urged shipowners and operators to avoid sending their ships through the strait. He said that doing so could expose the nearly 6,000 seafarers stranded in the Persian Gulf to “unnecessary danger.”

• Only two of the ships that transited on Tuesday took the Omani route, through which the U.S. Navy is providing guidance. The middle of the strait is considered dangerous because of the risk of mines laid by Iran’s military. Overall volumes of traffic were difficult to assess because many ships have turned off their location tracking devices.

Stock markets turn lower.

• Stock market investors have generally seemed more focused on the prospects for technology companies and the build-out of artificial intelligence systems than the effects of the war in Iran. But the latest burst of fighting in the Gulf appeared to rattle investors.

• The S&P 500 was down by about 0.3 percent at midafternoon. Shares of major tech companies have recently been hit by fears that enormous investments in A.I. systems may not pay off as handsomely as expected, with semiconductor companies coming under pressure in recent trading sessions.

• Stocks in Europe and Asia also fell on Wednesday, with declines accelerating as the fighting in the Gulf escalated.

• Still, many market strategists remain bullish. “The A.I. theme is intact, and strong earnings are on the way,” Louis Navellier, a longtime money manager, wrote in a research note. “The Iran situation still casts a shadow, with the chance for sudden high escalation still not out of the question,” he added, but an eventual resolution would be “a strong catalyst for a meaningful relief rally.”

Aruni Soni contributed reporting from New York.