nuclear program

WASHINGTON — After two weeks of war with Iran, the Trump administration is being forced to temper its expectations of a swift end to the conflict, with U.S. intelligence and defense officials expressing doubt it can achieve the overthrow of Iran’s government and the destruction of its nuclear program through military means.

It was an outcome forewarned by analysts at the State Department, the CIA and the Pentagon, who together alerted the administration to the pitfalls full-scale war with Iran would bring before President Trump decided to proceed, two U.S. officials told The Times, granted anonymity to speak candidly.

Certain military goals of Operation Epic Fury laid out at the start of the war are still seen as achievable at the Pentagon, with U.S. and Israeli strikes making steady progress degrading Iran’s ballistic missile infrastructure, its drone program and its navy.

But a prewar U.S. intelligence assessment, that an air assault was unlikely to topple the Islamic Republic, still holds, with the intelligence community now casting doubt the assault had any more political effect than to radicalize a government already devoted to the destruction of Israel and harming the United States.

A military procession in Tehran carries the casket of Ali Shamkhani, political advisor to Iran’s last Supreme Leader Ayatollah Ali Khamenei, who was also killed in U.S.-Israeli attacks.

(Atta Kenare / AFP/Getty Images)

Concern has only grown that Iran’s new government will make the fateful strategic decision to build a bomb after the war, unless Trump decides to escalate the conflict with a perilous ground invasion. And the White House now contends with a new mission imperative, created by its decision to launch the war itself, of reopening the Strait of Hormuz to vital shipping traffic that carries 20% of the world’s daily oil and liquid natural gas supply.

The foreign policy strategy Trump publicly laid out as his playbook for the conflict — to come down hard on the government, decapitating its leadership, and hope the remnants would seek mercy — has not worked, with Tehran looking for new ways to expand the war and maximize pain for the U.S. administration.

Trump has minimized the conflict as an “excursion” that would end “very soon,” while also calling it a war, vowing to take the time he needs to “finish the job.” He says it will conclude whenever he decides to end it.

It remains possible that a declaration from Trump that the fighting is over results in a ceasefire, as it did in June of last year, when Trump demanded an end to 12 days of war between Iran and Israel. But the Iranians have a vote, too — and senior leadership in the Islamic Republic have made plain they plan to continue fighting this time whether Trump likes it or not.

On Friday, the Pentagon announced that an additional expeditionary unit of 2,500 Marines was being deployed to the region to support the effort.

“Starting wars is an easy matter,” Ali Larijani, secretary of Iran’s Supreme National Security Council, wrote on social media. “Ending them does not happen with a few tweets.

“We will not leave you until you admit your mistake and pay its price,” he added.

It is a sore lesson for a president whose decade in public life has been distinguished by an exceptional ability to warp reality to his liking.

“The White House has created a dilemma for America: If it declares victory and ends the war, it leaves in place a weakened Iranian government with the means and renewed motivation to pursue nuclear weapons,” said Reid Pauly, a professor of nuclear security and policy at Brown University.

“If it presses on with the war,” Pauly added, “it risks the kind of mission creep that may eventually find American boots on the ground.”

In a news release last week, the White House said that, “from the opening hours of this historic campaign, the objectives were clear: obliterate Iran’s ballistic missile arsenal and production capacity, annihilate its navy, sever its support for terrorist proxies, and ensure the world’s leading state sponsor of terrorism will never acquire a nuclear weapon.”

Yet, at the start of the operation, Trump issued a promise to the people of Iran that, at the end of the U.S.-Israeli campaign, Iran’s military and paramilitary infrastructure would be so badly hobbled that a rare, generational opportunity would emerge for them to take their government back.

“To the great proud people of Iran, I say tonight that the hour of your freedom is at hand,” Trump said. “Stay sheltered. Don’t leave your home. It’s very dangerous outside. Bombs will be dropping everywhere. When we are finished, take over your government. It will be yours to take. This will be probably your only chance for generations.”

Trump said in the days that followed he would need to have a say over the next ruler, after assassinating the country’s longtime supreme leader, Ayatollah Ali Khamenei. But the Iranian system of clerics and militants defied the president, selecting in Khamenei’s son a man viewed as even more hostile to the West than his father was.

Israeli leadership, too, set out regime change as a goal of the war. Yet even their officials now say that a substantial leadership change in Tehran is an unlikely result.

Trump would go on to insist on the “unconditional surrender” from the Iranian government, a demand that he later said would be satisfied by the incapacitation of Iran’s military.

Repeating his conviction that the war will end soon, Trump told Fox News’ Brian Kilmeade in an interview Friday that he would order an end to the fighting “when I feel it. When I feel it in my bones.”

“The problem with the administration’s approach is that it has constantly shifted its goals. Some are achievable, such as degrading Iran’s conventional force. Others are not, such as picking the next leader of Iran,” said Ray Takeyh, a scholar on Iran at the Council on Foreign Relations.

“The mixed messages have led to confusion at home,” Takeyh added, “and lack of planning for oil shortages and getting the Americans out of the region shows that process and personnel can actually matter.”

Mark Dubowitz, CEO of the Foundation for Defense of Democracies, said the joint U.S.-Israeli campaign was always designed to unfold in three phases: degrading Iran’s ability to wage war, reducing Iran’s ability to repress democratic forces inside the country, and finally, encouraging the Iranian people to rise up.

“The president controls the strategy, but no president fully controls the endgame because the regime gets a vote,” Dubowitz said. “The endgame is not a scripted political transition directed from Washington. It is a regime under simultaneous military, economic, and internal pressure — to strip of its war-making and repression capabilities — and whether that produces succession, fracture, or collapse will ultimately be decided in Tehran.”

Whether the conflict will achieve the destruction of Iran’s nuclear program is an equally grave question in Washington, where officials are debating over a list of stark options on how to physically destroy, bury or retrieve the fissile material that Tehran could use to build a nuclear weapon — a threat seen as only more grave under the stewardship of an angry and vengeful government.

“The war was publicly justified, to the extent it was justified at all, in terms of destroying Iran’s nuclear program. Very few strikes have been directed against nuclear-related targets, however — almost certainly because those that survived last June’s attacks are invulnerable to air attack,” said James Acton, co‑director of the nuclear policy program at the Carnegie Endowment for International Peace.

“Unless the U.S. and Israel attempt high-risk special forces operations or a ground incursion,” he added, “Iran will end the war with its surviving nuclear infrastructure largely intact and greater incentives to build the bomb.”

Pauly agreed it is unrealistic to expect the United States and Israel can destroy Iran’s nuclear program through air power alone. The U.N. International Atomic Energy Agency believes Iran has roughly 440 kilograms — about 970 pounds — of 60% highly enriched uranium, possibly spread across multiple facilities.

“Securing this material will require either U.S. ground troops or, after some coercive bargain is reached, international inspectors,” Pauly said.

In an exchange with reporters last week at the Pentagon, Defense Secretary Pete Hegseth had few details to offer on what U.S. options were to remove or eliminate an accessible uranium stockpile, enriched to near weapons grade, that had been buried in a U.S. operation last year intended on obliterating the nuclear threat.

Diplomacy, he suggested, might be required to secure the material.

“I will say we have a range of options, up to and including Iran deciding that they will give those up,” he told reporters, “which of course we would welcome.”

WASHINGTON — Days after he was named Iran’s next supreme leader, and over a week since U.S. and Israeli bombing wiped out much of his family, Mojtaba Khamenei issued his first statement on Thursday demanding vengeance against the alliance over the war it unleashed.

He called on Iranian forces to continue thwarting vital shipping traffic through the Strait of Hormuz. He vowed to open new fronts against the United States and Israel. And he warned that Gulf states hosting U.S. bases would remain targets of Iranian attack.

Yet, what concerned the White House most was what the new supreme leader didn’t say.

Khamenei made no mention of a strategic endeavor that had brought the Islamic Republic to war: Its nuclear program, suspected for decades of harboring military dimensions.

The omission was not lost on officials in the Trump administration, who told The Times they are largely in the dark over the new supreme leader’s stance on whether Iran should break out to build a nuclear weapon.

Khamenei’s deep alliance with the Islamic Revolutionary Guard Corps, which has advocated for weaponization in the past, has raised concern that the new leader will depart from his father’s long-standing position against building a bomb.

U.S. intelligence assessments long held that the late ayatollah, Ali Khamenei, had adopted a strategy of remaining at the threshold of developing a nuclear weapon while avoiding the costs and risks of actually building one. In 2003, as the United States invaded Iraq over false claims that Saddam Hussein possessed weapons of mass destruction, Khamenei issued a religious edict — a fatwa — declaring nuclear weapons to be forbidden under Islam.

That doctrine is now in doubt, with the new supreme leader wounded and stewing underground over the U.S. assault that has devastated Iran’s military and killed his father, his mother and his sister, among other family members.

Concern among U.S. officials comes as Trump has expressed interest in ending the war “very soon,” even though a stockpile of uranium — a key ingredient in the construction of nuclear weapons — remains buried but accessible to Iranian authorities.

Defense officials are skeptical that the nuclear program can be fully dismantled without sending in a substantial U.S. ground force, an escalation that Trump has sought to avoid. But ending the war with Iran’s nuclear infrastructure partially intact could have devastating repercussions. The U.S.-Israeli campaign could force the new Iranian leader to conclude that regime survival requires a nuclear deterrent, one official said.

“Even if President Trump declares victory tomorrow, and points to the damage done to Iran’s conventional military, the fact of the matter is you have a more hardline regime in place with the key ingredients for a nuclear weapon,” said Eric Brewer, deputy vice president of the nuclear materials security program at the Nuclear Threat Initiative, who noted that Tehran still has a stockpile of 60% enriched uranium — close to weapons grade — and advanced centrifuges to take it over the finish line.

“What’s the plan for day after,” Brewer added, “as Iran starts to build back, and potentially seeks nuclear weapons?”

Patrick Clawson, director of the Iran program at the Washington Institute for Near East Policy, said that Mojtaba Khamenei’s position on the nuclear program has been a stubborn mystery. Reports spreading on social media that he opposed the Joint Comprehensive Plan of Action, a nuclear deal brokered among world powers and Iran during the Obama administration, are unsubstantiated, he said.

“While Mojtaba often advised his father on domestic issues, there is much less information about his position on foreign affairs, other than opposition to Israel,” Clawson said. “I have never seen any indications he took a position about the JCPOA.”

President Trump has outlined the destruction of Iran’s nuclear capabilities as a major goal. But in closed door briefings to Congress, defense officials have been less emphatic, according to Democratic lawmakers.

On Tuesday, shortly after Khamenei was named to succeed his father, Defense Secretary Pete Hegseth warned him to disavow continued nuclear work in an exchange with reporters.

“He would be wise to heed the words of our president, which is to not pursue nuclear weapons,” Hegseth said, “and come out and state as such.”

Israel and the United States launched an air campaign against Iran on Saturday, striking Tehran and several other cities in what President Trump said was the start of “major combat operations.”

The attacks began with Israeli strikes Saturday morning — a workday in Iran — on Tehran, the capital, with residents speaking of attacks near the presidential palace and Iran’s National Security Council.

There were also reports of Israeli strikes on the Ministry of Intelligence, Ministry of Defense, the Atomic Energy Organization of Iran and a military complex.

Israel’s defense minister said the “pre-emptive strike” was to “remove threats against the State of Israel”.

It remains unclear the extent of the campaign and what its ultimate aim will be. But in an eight-minute recorded video message on Truth Social, Trump outlined a maximalist strategy that would see much of what he called “this very wicked, radical dictatorship from threatening America and our core national security interests.”

“We are going to destroy their missiles and raze their missile industry to the ground. … We are going to annihilate their navy. We are going to ensure that the region’s terrorist proxies can no longer destabilize the region or the world, and attack our forces,” he said. “And we will ensure that Iran does not obtain a nuclear weapon.”

He urged Iranians to take over their government.

“This will be probably your only chance for generations,” he said. “For many years, you have asked for America’s help, but you never got it. No president was willing to do what I am willing to do tonight.”

Trump also said U.S. military forces “may have casualties.”

Iran’s IRNA news agency quoted a source in the presidential office who said Iranian President Masoud Pezeshkian was unharmed in the strike.

Besides the capital, explosions could be heard in other the cities, including Isfahan, Karaj, Kermanshah and Qom, according to Iranian state media.

Both Israel and Iran shut down their airspace.

Cellphone and internet communications were disrupted shortly after the attacks began. Multiple Iranian state news websites also appear to have been hacked.

There was no immediate official response from Iran, but Ebrahim Azizi, the head of the Iranian parliament’s national security commission, vowed retaliation.

“We warned you!” he wrote on social media. “Now you have started down a path which end is no longer in your control.”

Residents reported hearing sounds of missiles flying over cities in Jordan, Syria and Lebanon in what was thought to be a missile barrage from Iran against Israel.

The attacks come two days after the U.S. and Iran concluded a third round of Oman-brokered negotiations in Geneva aimed at reducing tensions and stopping the prospect of war.

On Friday, Trump expressed displeasure with the pace of the talks, saying the Iranian side were not negotiating in “good faith” or giving in to U.S. demands. But Oman’s Foreign Minister Badr Albusaidi said a deal was “within reach.”