Breakthrough, Aided by Israel

It took months for the beacons to do their work and report home, complete with maps of the electronic directories of the controllers and what amounted to blueprints of how they were connected to the centrifuges deep underground.

Then the N.S.A. and a secret Israeli unit respected by American intelligence officials for its cyberskills set to work developing the enormously complex computer worm that would become the attacker from within.

The unusually tight collaboration with Israel was driven by two imperatives. Israel’s Unit 8200, a part of its military, had technical expertise that rivaled the N.S.A.’s, and the Israelis had deep intelligence about operations at Natanz that would be vital to making the cyberattack a success. But American officials had another interest, to dissuade the Israelis from carrying out their own pre-emptive strike against the Iranian nuclear facilities. To do that, the Israelis would have to be convinced that the new line of attack was working. The only way to convince them, several officials said in interviews, was to have them deeply involved in every aspect of the program.

Soon the two countries had developed a complex worm that the Americans called “the bug.” But the bug needed to be tested. So, under enormous secrecy, the United States began building replicas of Iran’s P-1 centrifuges, an aging, unreliable design that Iran purchased from Abdul Qadeer Khan, the Pakistani nuclear chief who had begun selling fuel-making technology on the black market. Fortunately for the United States, it already owned some P-1s, thanks to the Libyan dictator, Col. Muammar el-Qaddafi.

When Colonel Qaddafi gave up his nuclear weapons program in 2003, he turned over the centrifuges he had bought from the Pakistani nuclear ring, and they were placed in storage at a weapons laboratory in Tennessee. The military and intelligence officials overseeing Olympic Games borrowed some for what they termed “destructive testing,” essentially building a virtual replica of Natanz, but spreading the test over several of the Energy Department’s national laboratories to keep even the most trusted nuclear workers from figuring out what was afoot.

Those first small-scale tests were surprisingly successful: the bug invaded the computers, lurking for days or weeks, before sending instructions to speed them up or slow them down so suddenly that their delicate parts, spinning at supersonic speeds, self-destructed. After several false starts, it worked. One day, toward the end of Mr. Bush’s term, the rubble of a centrifuge was spread out on the conference table in the Situation Room, proof of the potential power of a cyberweapon. The worm was declared ready to test against the real target: Iran’s underground enrichment plant.

“Previous cyberattacks had effects limited to other computers,” Michael V. Hayden, the former chief of the C.I.A., said, declining to describe what he knew of these attacks when he was in office. “This is the first attack of a major nature in which a cyberattack was used to effect physical destruction,” rather than just slow another computer, or hack into it to steal data.