The intelligence community appears to have had good reason to believe Iran paused this program. U.S. officials, anonymously, have suggested that the United States intercepted oral and written communications documenting the "halt." There are also indications in the open-source literature. In 2005, Hassan Rowhani, Iran's top nuclear negotiator for the first few years of the nuclear crisis, gave a pair of remarkable talks in which he recounted the decision-making behind Iran's engagement with the West. Iran's leaders engaged in an intense internal debate through much of 2003, reorganizing the decision-making structure for Iran's nuclear programs. Rowhani even refers obliquely to Fakhrizadeh's PHRC, noting the problems arising from the activities of a "private entity" that Iran did not wish to disclose to the International Atomic Energy Agency (IAEA).
Pausing the program is certainly what I would have done. Iran preserved the ostensibly civilian aspects of its nuclear program, including a large centrifuge facility near Natanz, that would allow it to make technical progress toward a bomb capability, while attempting to hide evidence of the parallel program that might get it bombed. So, for example, Iran closed up shop at Lavizan and, when the IAEA asked to visit, sent in the bulldozers and declined to make Fakhrizadeh available for interviews. Today, the site of Iran's covert nuclear weapons program is a lovely park.
The second important idea in the 2007 NIE relates to why Iran shut down Fakhrizadeh's little bomb empire. The Iranians would have you believe that the supreme leader declared nuclear weapons to be a sin; the U.S. intelligence community believes it was more likely due to "international scrutiny and pressure." That's an important observation. Left to its own devices, the 2007 NIE suggests, Iran would likely have acquired a nuclear weapon. As it is, Iran was continuing work in areas that it could claim had a legitimate civilian purpose, while holding off on any overt moves toward weaponizing its growing nuclear capabilities. The NIE was not intended to give Iran a clean bill of health; it was intended to signal to policymakers observable evidence that Iran was sensitive to international pressure. As Thomas Fingar, the former head of the National Intelligence Council explained, he and his co-authors intended it to send the message: "You do not have a lot of time, but you appear to have a diplomatic or nonmilitary option."
This is the core observation of the 2007 NIE: Iran had both a civil enrichment program at Natanz, as well as a parallel weapons program that was centered on the PHRC at Lavizan. Under international scrutiny in 2003, Iran sought to close down the parallel program, putting Fakhrizadeh and his cronies on ice, while preserving a civilian program that would allow Iran to pursue a bomb at a later date if it so chose.
I am baffled by the ire that conservative pundits have directed at the 2007 NIE. For a group of people who believe that Iran had a covert nuclear weapons program and who support sanctions on Iran, the 2007 NIE ought to be welcomed with open arms. Because, you know, it says Iran had a covert nuclear weapons program and that sanctions might work. I normally don't do the "pox on both houses" thing, but in this case I am also baffled by the embrace of the NIE by those opposed to sanctions on Iran. If the document said one thing, it was that international pressure, like sanctions, is important to preventing a nuclear-armed Iran.
Since 2007, the debate within the intelligence community has been about whether Iran has restarted its covert nuclear weapons program. In February 2011, the United States completed another NIE, which confirmed the view that Iran had not restarted the parallel program, though U.S. officials made clear in stories with the Wall Street Journal and Washington Post that they were carefully watching the remnants of Fakhrizadeh's empire.
The intelligence community faces a real challenge in determining whether SPND oversees an active or dormant nuclear weapons program. Take the explosives facility near Parchin. In the past few years, the IAEA has been interested in some explosives work carried out with the assistance of a former Soviet nuclear weapons scientist. His specialty was making the conventional explosives that perfectly compress a sphere of plutonium or highly enriched uranium at the heart of a bomb. After the fall of the Soviet Union, this scientist took the same process for compressing plutonium and applied it to making nanodiamonds (really, really small diamonds for industrial applications).
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