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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.”

President Trump was uncommonly lucky in his first term, neither inheriting nor provoking a crisis of the sort that tests U.S. presidents, until COVID struck in his final 10 months. (He failed that test, contributing to his 2020 reelection defeat.) Trump 1.0 was bequeathed a growing economy from President Obama, and the incoming president assembled a roster of capable advisors who often acted to prevent him from doing nutty things at home and abroad.

Trump 2.0 made sure that no such human guardrails populated his second Cabinet, only genuflecting enablers. Unrestrained, he has presided over one crisis on top of another, all of his own making. Tariff mayhem and high prices. Armed agents and troops in American cities. Repeated violations of court orders. Demolition at federal agencies and the White House.

And now Trump has taken the nation to war against Iran in league with Israel’s Benjamin Netanyahu. Depending on the moment and the audience, a contradictory Trump is either claiming the war is “very complete” or that much remains to be done to “decimate” Iran. On Wednesday he blithely told Axios, “Any time I want it to end, it will end,” even as U.S. officials planned further actions.

In any case, Trump’s war of choice and the killing of the supreme leader of Iran’s terroristic theocracy now has spawned another potential crisis, counterterrorism experts warn: the risks of retaliatory terrorist threats at home. And that is a threat, whether from homegrown extremists or sleeper cells of the sort that came alive for 9/11, that is likely greater because of the initial self-induced crisis of Trump’s second term: his whacking of the federal government.

Trump authorized Elon Musk’s destruction of the bureaucracy in the name of “government efficiency” and continues to exact retribution against any federal employee who had anything to do with investigating and prosecuting him during his interregnum. Longtime agents and operatives have been eliminated at the FBI, Justice Department, Department of Homeland Security, CIA and elsewhere. Especially at the FBI, counterterrorism experts with centuries of collective experience are gone and many who remain have been diverted to Trump’s top priority: mass deportations.

Consequently, the president who promised to “Make America Safe Again” has arguably made Americans less safe.

I raised this scary prospect just over a year ago as Trump’s teardown of the purported Deep State was underway. And now a Mideast war that Trump promised never to start has further incentivized Iran and its jihadi proxies to hit back, just as he’s diminished the nation’s early-warning systems.

Enough intelligence remains, however, that even in the days before Trump ordered the first strikes against Tehran, government analysts were picking up “worrisome signs” of Iranian plotting against U.S. targets, the New York Times reported. After the U.S.-Israel onslaught and death of Ayatollah Ali Khamenei on Feb. 28, the government intercepted a possible Iranian “operational trigger” to “sleeper assets” outside Iran, according to ABC News.

Counterterrorism expert Colin P. Clarke, executive director of the Soufan Center, which focuses on global security and transnational terrorism, wrote this week in the Atlantic that U.S. agencies’ record of disrupting Iranian-backed plots in America was in jeopardy given the recent changes in funding, personnel and priorities. “Because of this,” he concluded, “the U.S. homeland is arguably more vulnerable than it has been in a long time.”

In a follow-up exchange of emails, Clarke told me, “Many of this administration’s moves have been myopic — shifting counterterrorism resources to immigration, firing FBI agents working counterintelligence, etc. A week before the U.S. went to war with Iran, the FBI Director Kash Patel was off gallivanting in Milan at the Olympics [where he struggled to chug a Michelob Ultra, a firing offense in its own right] when he should have been preparing for the potential for an Iranian response on U.S. soil.”

Patel’s preposterous partying with the U.S. men’s hockey team while war-planning was underway in Washington was widely, justifiably mocked. But it stands as a metaphor for the entire Trump administration’s cavalier attitude toward homeland security. Its abusive focus on both migrants and citizens protesting on the migrants’ behalf is a distraction from actual threats to the country.

Patel, like his boss at the Justice Department, Atty. Gen. Pam Bondi, has made plain in words and actions that the president’s political enemies are the real public enemies No. 1. One of Bondi’s first acts was creation of a “weaponization working group” to identify, fire or prosecute those in her department who’d investigated and prosecuted Trump, many of whom also had experience in domestic and transnational terrorism. The association representing FBI agents called her purges “dangerous distractions” from the work “to make America safe again.”

Days after starting the Iran war, when homeland security should have been on red alert, Trump fired his secretary of Homeland Security, Kristi Noem. Her costly cosplaying as the homeland’s heroine on horseback in anti-migrant videos, along with her penchant for luxury jets allegedly to transport deportees, was too much even for him.

Yet all three “national security” officials — Noem, Bondi and Patel — simply reflect Trump’s own warped approach and blasé attitude toward the homefront.

When Time magazine last week asked the commander in chief whether Americans should be worried about potential terrorist strikes at home, he replied, “I guess.”

“We plan for it,” he added. “But yeah, you know, we expect some things. Like I said, some people will die. When you go to war, some people will die.”

The administration is planning for it all right. An extraordinary number of senior Trump officials have taken up residence in houses on military bases, including Bondi, Noem, the secretaries of State and Defense, Marco Rubio and Pete Hegseth, and White House consigliere Stephen Miller.

The rest of us just have to keep our fingers crossed. I guess.

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