Diplomacy and Sanctions, Yes. Left Unspoken on Iran? Sabotage.

WASHINGTON — President Obama and Secretary of State John Kerry have a simple explanation for their surprising success in getting Iran to dismantle much of its nuclear infrastructure, ship out 98 percent of its nuclear fuel and release five American prisoners: Patient diplomacy, backed by escalating economic sanctions, accomplished more than military action ever could have.

When the final history of this remarkable encounter between Washington and Tehran is written, the story is likely to be far more complex.

Yes, diplomacy and economic pressure were critical, but even several of Mr. Obama’s top aides doubted as recently as a year ago that, in the end, Iran’s mullahs and generals would actually dismantle a program in which they had invested both national pride and billions of dollars. Those aides had good reason for skepticism: While all comparisons between North Korea and Iran are fraught, if economic pressure alone could do the trick, Pyongyang would have given up its nuclear program two decades ago.

But Mr. Obama’s strategy had a major coercive element as well. This included covert actions that repeatedly, if briefly, set back the nuclear program and convinced Iranian elites that its secrecy had been compromised. Then there was the fear, in Washington and Iran, that Prime Minister Benjamin Netanyahu of Israel would launch a pre-emptive attack.

Mr. Obama has almost never talked about that side of the campaign, the short-of-war coercion that was part of what his aides once called the “light footprint strategy” of avoiding full-scale military action. But he alluded to its success obliquely on Sunday when he expressed pride in the fact that “we’ve achieved this historic progress through diplomacy, without resorting to another war in the Middle East.”

By some accounts, it was a close call.

Michael D. Morell, a former C.I.A. deputy director, declines to talk about the actions taken against Iran but says that as Iran’s program accelerated in Mr. Obama’s first term, conflict loomed. “Before the negotiations for the nuclear deal began,” he said, “we were closer to war with the Islamic Republic than at any time since 1979.”

The chances of war breaking out over the Iranians’ nuclear program were higher in the Obama administration than they were during the George W. Bush administration that preceded it, if the public and private accounts of dozens of officials who served in one or the other — and a few in both — are to be believed.

Mr. Bush, wrapped up in two wars already and his credibility on going after weapons of mass destruction so destroyed after the 2003 Iraq invasion, never seriously contemplated military action against Iran. When his vice president, Dick Cheney, advocated bombing a secret nuclear reactor in Syria in 2007, partly to make a point to Iran, Mr. Bush rejected the proposal out of hand, a tale Mr. Cheney tells with some bitterness in his memoir.

During Mr. Bush’s last year in office, Israel sought — and was denied, again over Mr. Cheney’s objections — the bunker-busting bombs and other equipment it needed to carry out an effective strike on Iran. It took Israel years to develop its own lesser ability, and during Mr. Obama’s tenure, according to the recent memoirs of a former Israeli defense minister, Ehud Barak, Mr. Netanyahu nearly pulled the trigger three times, coming closest in 2012. “We planned to do it,” Mr. Barak said.

Mr. Obama had little doubt that if Israel started a conflict, the United States would be unable to stay out. That was the conclusion of a series of classified war-gaming exercises conducted at the National War College, at the Pentagon and inside American intelligence agencies.

In public, Mr. Obama credits the broad sanctions regime — which Mr. Netanyahu at first warned would never work — for convincing Iran’s Ayatollah Ali Khamenei and other hard-liners that they had to pursue another path. Certainly it played a major role in Iran’s calculus, as oil shipments dropped by more than half and Iranian tankers bobbed at sea for more than a year, unable to deliver their goods.

Mohammad Javad Zarif, the Iranian foreign minister, has repeatedly argued that the “unjust sanctions” were counterproductive, noting that Iran’s number of centrifuges and its fuel stockpile expanded as the economic noose tightened. But eventually, the price became too high.

What Mr. Obama does not say — because he cannot without describing classified programs — is that many of his own aides believe that an American covert sabotage program that began in the Clinton administration and steadily escalated over the next 15 years also played a critical role in persuading the Iranians to cash in the program.

Court records that were made public in the prosecution of the Tinner family in Switzerland, a supplier of nuclear equipment to Libya, Iran and other countries as part of the Pakistani scientist A. Q. Khan’s black market in atomic technology, made it clear that the C.I.A. had recruited insiders to provide the Iranians with faulty goods. In 2006, power supplies for the country’s centrifuges blew up; it turned out they had been diverted, and tinkered with, by the United States before they were delivered.

The assassination of Iranian nuclear scientists, widely assumed to be the work of Israel’s Mossad, grew so intense at one point that Hillary Clinton, then the secretary of state, publicly denounced the killings, being careful not to name Israel.

Mr. Bush authorized, and Mr. Obama accelerated, perhaps the best-known piece of covert action: the broad cyberattacks against the Natanz nuclear enrichment site in Iran, using what became known as the Stuxnet computer worm. Despite its sophistication — and the roughly 1,000 centrifuges destroyed — it probably slowed the program for only a year or so.

But the operation, code-named Olympic Games, made it clear to the Iranian elite that the United States and Israel were deeply inside their program, and clearly had turned some scientists and other workers who helped get the destructive code into the nuclear facilities.

It may be years before anyone knows for sure how much of a role these tactics played in Iran’s ultimate decision. It might be that Iran would have given up the program anyway, given enough time. But in commentary published Tuesday, Graham Allison of Harvard, who wrote the definitive history of the Cuban missile crisis, engaged in some what-might-have-happened speculation if Mr. Obama’s diplomatic, economic and coercive effort had not worked.

If Mr. Netanyahu had succeeded in killing the deal, or Republicans in Congress had blocked it, the sanctions “would have collapsed,” he said. As Iran sped closer to a bomb, the Israelis would have renewed their threat to attack, and Republican candidates for president would blame Mr. Obama “for having failed to prevent Iran’s acquiring a bomb.”

The world, Mr. Allison concluded, “could well have been on the brink of a third major war in the Middle East.”