Much of Iran’s Nuclear Program Remains After Israel’s Strikes. At Least for Now.

Israel badly damaged one of Iran’s key nuclear sites and killed a startling array of top military and nuclear officials in the attacks that started on Friday morning. But when the sun rose after that devastating assault, it was also clear how much of Iran’s nuclear program remained, at least for now.

The Israeli strikes appear to have destroyed an aboveground nuclear fuel production site and electrical supply centers at Iran’s largest uranium enrichment center, at Natanz. The killing of some of Iran’s top nuclear scientists continues a long-running Israeli campaign targeting the expertise needed to build a bomb. But the first phase of the Israeli attacks did not hit the most likely repository of Iran’s near-bomb-grade nuclear fuel — and that may have been deliberate.

That stockpile is stored at a vast complex outside the ancient former capital of Isfahan, according to international inspectors who are charged with measuring and monitoring it. Israel’s 100 fighters and swarms of missiles and drones stayed away from Isfahan in their first wave, even though it is one of the largest nuclear sites in the country and, according to Western intelligence services, one of the centers of Iran’s secret weapons research programs.

The Israel Defense Forces issued a news release on Friday afternoon saying that in a second wave of attacks, it had hit Isfahan, but not the fuel stockpile. Instead, it focused on laboratories that worked on converting uranium gas back into a metal — one of the last stages of building a weapon. But it said nothing about hitting the area where the fuel itself is stored.

“We saw the fuel there just recently,” Rafael Mariano Grossi, the director general of the International Atomic Energy Agency, the United Nations organization that tracks fuel to make sure it is not diverted to weapons projects, said on Friday, a few hours after the attacks began. Inspectors were inside the Isfahan facilities over the past few weeks, conducting the final inventories for the quarterly report on Iran’s capabilities that was distributed to the agency’s board this month, as it focused on Iran’s compliance with inspectors’ demands.

The mystery is why Israel avoided hitting the stockpile, which gives Iran its fastest pathway to producing a small nuclear arsenal. And it was the core of Prime Minister Benjamin Netanyahu’s justifications early Friday for ordering the strike, after two decades in which Israel has always stopped short of pulling the trigger.