Iran's Nuclear Program: Destroyed or Just Hidden?

The tunnel entrances at Isfahan are open. The satellite images show it clearly. So when President Trump declared that Iran's nuclear material was buried deep underground and "unusable," someone forgot to tell the Iranians.

Forty days after Ali Khamenei was killed in US-Israeli joint strikes, his son Mojtaba now hangs in portrait form over Tehran's streets. Six weeks of war have reshuffled Iran's leadership, battered its missile arsenal, and — according to Washington — eliminated its nuclear program entirely. But the original justification for this conflict is increasingly looking like the war's most unresolved question.

To cut through the noise, PRISM spoke with Jeffrey Lewis, professor at the Middlebury Institute's James Martin Center for Nonproliferation Studies and one of the world's leading open-source analysts of nuclear capabilities.

His assessment is not reassuring.

Half the Uranium Is Accounted For. What About the Other Half?

The US government is not speaking with one voice on Iran's nuclear future. Secretary of Defense Pete Hegseth insists the program will be fully dismantled. Benjamin Netanyahu echoes the demand. But Vice President JD Vance, currently leading ceasefire talks in Pakistan, has signaled he's less concerned about Iran's enrichment rights. And Trump himself has suggested the whole question is moot — Iran's program is already irreparably destroyed.

Lewis finds that last claim particularly hard to square with the evidence. "There's no evidence of that," he says flatly. "The tunnels are intact. The Iranians buried the entrances to protect them, but we've seen them open those entrances and access the tunnels. If you put something in a safe in your house, it doesn't mean you can't get to your money. You just have to open the safe."

The deeper problem is one of incomplete accounting. US officials have claimed that roughly half of Iran's highly enriched uranium stockpile is located at the underground tunnel complex in Isfahan. But Lewis asks the obvious follow-up: "So where's the other half? Is some of it still at Fordow and Natanz? Is it at some third location? What about their ability to produce centrifuges? What about centrifuges they have in storage? What about the people who know how to operate them?"

Physical destruction, he argues, is not the same as elimination. "You can set them back by destroying things, immobilizing things, and taking things. But there's a large group of people who understand how to operate these things. There's a basic capability that's in place."

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There's an additional irony that Lewis doesn't let pass. The country currently mediating the ceasefire — Pakistan — is the same country that originally supplied Iran with its centrifuge technology, through the AQ Khan proliferation network. "What's the plan here, guys?" he asks.

Surveillance Has Limits. So Does Confidence.

A common counterargument runs like this: even if Iran's nuclear material isn't fully destroyed, the country is under such intense surveillance that any attempt to reconstitute the program would be detected and stopped immediately. Lewis is skeptical of that confidence.

"The intelligence penetration was real. Is it still real? No one knows that." Satellite coverage, he notes, is not continuous — images are captured at intervals, and without around-the-clock drone surveillance over specific sites, there are windows of opportunity. "Unless we are operating drones 24/7 over those sites, we're not going to be able to know for certain unless the Iranians are really slow."

The historical record supports his caution. When Iran opened its tunnel entrances back in September and October of last year, the US and Israel observed it — and did nothing. "It's also true that we saw them opening up the tunnels back in September and October, and we didn't do anything about it."

Lewis is careful not to overstate his case. He's not claiming Iran is actively reconstituting its program. He's making a narrower, more uncomfortable point: the certainty with which US and Israeli officials speak about knowing where all the material is, and being able to detect any movement of it, is not warranted by the intelligence picture as he understands it.

The Lesson Every Proliferator Is Taking Notes On

Perhaps the most consequential dimension of this conflict isn't what happens to Iran's nuclear program — it's what other countries conclude from watching it unfold.

Lewis doesn't hesitate when asked what lesson potential nuclear proliferators will draw. "That it makes sense to finish that nuclear weapon as soon as you can."

His reasoning is blunt. Three countries have, in different ways, made disarmament agreements with the United States: Iraq, Libya, and Iran. "The US double-crossed all of them." Meanwhile, North Korea held onto its weapons and remains, by any measure, more secure than any of the three. Pakistan, nuclear-armed, is currently hosting the US Vice President for ceasefire talks. "I'd rather be North Korea or Pakistan than Iran, Iraq, or Libya."

This is not merely an academic observation. It is a direct challenge to the foundational logic of nuclear nonproliferation: that states which give up weapons programs, or agree not to pursue them, will receive security guarantees in return. If that bargain is no longer credible — and the evidence from the past two decades suggests it may not be — the entire architecture of the nonproliferation regime is under strain.

The nuclear taboo itself came up during the conversation. When Trump's rhetoric last Tuesday escalated to the point where the White House had to explicitly deny considering nuclear weapons use, Lewis was watching carefully. He didn't interpret it as a genuine nuclear threat. But he noted, with evident unease, that nuclear weapons would actually be militarily useful for destroying deep underground facilities like Isfahan. "I'm glad that the US has not used them, and I think it would be a terrible mistake to do that. But there's still a taboo there, and I don't know how strong that taboo is."