There are still many more questions to answer. But the fact that so many thoughtful people are expressing concern about what this NIE really means, and what has happened since it was released, gives this document a new level of significance. It has also fundamentally altered the United States’ posture towards Iran, in ways that we’re only beginning to understand.

While not refuting the judgment of his intelligence agencies that Iran halted the third leg, a set of covert, military-run nuclear weapons activities, McConnell clearly wanted to tamp down the dramatic headline of the recent National Intelligence Estimate, which gave the strong impression that Iran’s nuclear program is, at least temporarily, on ice.

We judge with high confidence that in fall 2003, Tehran halted its nuclear weapons design and weaponization activities, as well as its covert military uranium conversion and enrichment-related activities, for at least several years. Because of intelligence gaps, [the Department of Energy] and the [National Intelligence Council] assess with only moderate confidence that all such activities were halted. We assess with moderate confidence that Tehran had not restarted these activities as of mid-2007, but since they comprised an unannounced secret effort which Iran attempted to hide, we do not know if these activities have been restarted.

For good measure, McConnell added, “I note again that two activities relevant to a nuclear weapons capability continue: uranium enrichment that will enable the production of fissile material and development of long-range ballistic missile systems.”

This is now the official counterargument to the NIE. The fact that these statements come from the man who is ultimately responsible for that document is, as best I can tell, unprecedented.

Who is out there actually defending the NIE? Israel now joins the French, the President of the United States, and the U.S. Director of National Intelligence in concluding that Iran is still on the path to a nuke, despite the NIE’s judgment that Iran halted its nuclear weaponization program years ago. Like the other NIE skeptics, Israel homes in on two key pillars of a nuclear program, including uranium enrichment and ballistic missile construction, and concludes that Iran’s nuclear ambitions are alive and thriving. (President Bush made this case publicly, as well.)

Israel’s departure with the NIE differed in that it rebuked the document itself as diplomatically counterproductive, something that, so far, only staunch critics of the intelligence community in the United States have done. Israel’s reaction is hardly surprising, of course, given its particularly precarious position in the region, and its long-standing insistence that Iran is either close or very close to developing a nuclear weapon.

But the fact that Israel is now on record against the U.S. conclusion is an important development, and could signal the start of a new international alliance, backed by President Bush himself, against the NIE’s conclusion, which will continue to be painted as rosy, overly optimistic, and fundamentally off-the-mark because it doesn’t rank the enrichment and missile programs highly enough in the final calculation. Will the authors of the NIE defend their work again, as they did so forcefully when their key judgments were declassified late last year? Stay tuned.

In the meantime, here’s something from the vault on Israel’s historic insistence that Iran was practically within reach of a nuke. In October 2006, I sat in on a meeting between then-Congressman Curt Weldon, a Pennsylvania Republican, and Daniel Ayalon, then Israel’s ambassador to the United States. (I was writing a profile of Weldon, and the two men had previously scheduled this meeting in Weldon’s office.) The conversation turned to Iran’s nuclear ambitions, a topic that had possessed Weldon’s interest. Like the Israelis, he insisted that Iran was closer to a weapon than most people thought, and that the United States perilously underestimated the regime.

Weldon told Ayalon that Iran would have a nuclear weapon in two years. A military attaché who had accompanied Ayalon to the meeting replied, with a smile, “We say less.” It was a chilling moment, in and of itself. But it also stood out because, at the time, such a dire assessment was at odds with most experts’ opinion, as well as the judgment of the CIA and other U.S. intelligence agencies. They estimated then that Iran’s weapons program was at least five years from maturity and probably more, given Iran’s difficulty producing the necessary materials for a bomb. It’s worth noting that, around the time of this meeting, the intelligence community would have been in the early stages of its reassessment of the Iranian program, which resulted in last year’s NIE and the about-face on the previous assessment.

Herve Morin, the French defense minister, was in Washington yesterday, and he said that “coordinated information from a number of intelligence services leads us to believe that Iran has not given up its wish to pursue its [nuclear] program,” and is “continuing to develop” it. Morin (unsurprisingly) called upon the International Atomic Energy Agency to “continue carrying out all the necessary investigations” into Iran’s nuclear activities. The IAEA has also doubted U.S. intelligence.

The French dissent is significant on a number of levels. First, France is a key ally in the administration’s hard line against the Iranian regime, and having their defense minister sound such a provocative note of caution could help put the wind back in the administration’s sails as it tries to rally international pressure on Iran. When the NIE reversed earlier claims that Iran was pursuing a nuclear weapon, it presumably undercut the administration’s push to impose harsher international sanctions on Iran.

Second, note that Morin said “a number of intelligence services” had provided information that led France not to concur with the United States’ key judgments—ones, it should be noted, that the president sought to distance himself from the very day they were declassified. France is saying that a community of nations, which certainly includes Israel, have pooled their notes, and that they find plenty of reason to believe the United States is missing the mark. This contrary assessment probably hinges on Iran’s continued pursuit of enriched uranium, as well as its ongoing ballistic missile program. (See my previous post on how President Bush homed in on these legs in Iran’s nuclear platform.) France has expressed great concern over Iran’s pursuit of ballistic missiles, which could threaten Israel and U.S. bases in the Middle East.

The Russian and Chinese governments—whose support for sanctions is key at the United Nations—haven’t come out in opposition to the NIE, but it doesn’t hurt President Bush’s case to keep up the pressure by having a key European ally come over to his side, especially one that feels threatened by Iran. The United Nations Security Council this week considered a new proposal from the United States and France, among others, for new sanctions against Iran.

President Bush offered fresh evidence in his State of the Union address last night that not all decision-makers share the intelligence community’s view on Iran’s nuclear ambitions. Although he was remarkably restrained in his rhetoric–particularly in comparison to years past–Bush homed in on Iran’s uranium enrichment and ballistic missile programs to remind us that the country still poses a mortal threat.

Tehran is also developing ballistic missiles of increasing range and continues to develop its capability to enrich uranium, which could be used to create a nuclear weapon. [Note: The recent National Intelligence Estimate on Iran's nuclear program doesn't contradict him on this point.] … Our message to the leaders of Iran is also clear: Verifiably suspend your nuclear enrichment, so negotiations can begin. And to rejoin the community of nations, come clean about your nuclear intentions and past actions, stop your oppression at home and cease your support for terror abroad. But above all, know this: America will confront those who threaten our troops, we will stand by our allies and we will defend our vital interests in the Persian Gulf.

The NIE concluded that Iran halted its nuclear weapons program in 2003, but it narrowly defined said program as “Iran’s nuclear weapon design and weaponization work,” as well as its covert work to convert and enrich uranium. In other words, this assessment does not cover Iran’s civilian enrichment work, which holds so-called “breakout potential” for a weapons program, nor does it cover work on building a missile to deliver a bomb. Still, it seems the community’s view is that a full weapons program cannot come to fruition without the key weaponization piece.

The president, though, clearly thinks otherwise, and he’s not alone. No less than the Director of National Intelligence, Mike McConnell, said recently that he thinks–apparently despite the NIE’s findings–that Iran is on the path to obtaining a nuclear weapon.

This all could be evidence of a high-level split between the intelligence community and its customers. But there’s another possibility. Intelligence is a special policy input, but it is, in the end, just one input. It’s usually a mistake to take any single NIE or intelligence stream as dispositive. The president learned that painful lesson in the run-up to war in Iraq. Some might find it refreshing that this administration, even if in its final days, is not once again hanging its policy towards a key Middle Eastern country on inherently murky intelligence. It just may be that this time the country in question actually does have nuclear weapons, despite what the intelligence community believes.

While I hate to say the piece didn’t do much to illuminate McConnell’s character, it also may have buried the lead. In the third to last paragraph of the 18-page article, the DNI drops what I consider a mini-bombshell: He thinks that Iran “is on the path to get a nuclear weapon.”

That assessment stands in contrast to the intelligence community’s official, coordinated judgment that Iran shut down its nuclear weapons program in the fall of 2003. That was the remarkable turn-about contained in the unclassified key judgments of the National Intelligence Estimate on Iran, which McConnell released–after publicly vowing not to–last month.

Now, the NIE was uncertain about whether Iran was restarting its nuclear weapons program, and it certainly left open the possibility, but it seems to me a dramatic public pronouncement for the DNI to say he personally believes there’s no doubt about Iran’s intentions.

Here’s the passage in question from Wright’s article.

When we last spoke, McConnell said, ‘There’s no doubt in this observer’s mind that Iran is on the path to get a nuclear weapon. It will force an arms race in the region.’

As Wright chronicles in his piece, McConnell has recently shown a tendency to say things off-the-cuff that turn out to be not quite accurate, but this statement is rather emphatic. Indeed, the term “no doubt” is a much bolder assertion than the intelligence community’s mark of “high confidence,” used in NIEs to indicate that the assessment is based on high-quality information. One has to presume that, as the nation’s top intelligence official, McConnell has access to the very best information. So what does he know that we don’t after reading the NIE?

For background on the build-up to the NIE’s release, see my story from National Journal last month, “The Other About Face on Iran.”

“You will be disappointed,” Mike McConnell, the director of national intelligence, told a gathering of journalists in Washington on November 13. U.S. spy agencies were putting the finishing touches on a National Intelligence Estimate about Iran’s nuclear intentions and capabilities, which included new leads that the agencies had been vetting since spring. But departing from recent practice, McConnell said, “I do not intend to release unclassified key judgments” of the NIE, those heavily edited yet potentially telling morsels of analysis that might ultimately show how close the United States is to a war with Iran.

“We have probably done a thousand of these” NIEs, he said. “We have done unclassified key judgments for maybe three. So we created an expectation that we do this, because we did it previously.” And that was a bad idea, McConnell said, with some passion.

For starters, even the “sanitized” version of an NIE could compromise vital sources and methods, he said, because the target of the estimate is, of course, going to read the document. Second, “I don’t want to have a situation where the young analysts” — whom McConnell guards with particular devotion because he was once one of them — “are writing something because they know it’s going to be a public debate or political debate. They should be writing it to call it as it is.”

McConnell, whom a longtime colleague describes as having “not a political or manipulative bone in his body,” also stated he would “make every effort” to prosecute anyone who leaked the NIE. Then, he vowed (twice) to resign if the intelligence was “cherry-picked in an inappropriate way” by government officials.

Things changed dramatically in the three weeks after McConnell’s public denunciation of leaks and declassification. On December 3, McConnell and his aides reversed that decision and released the unclassified key judgments of the NIE on Iran. Try as McConnell might to keep the lid on the new estimate, his lieutenants were influenced by the political realities of intelligence these days.

“They thought it would leak and be distorted, and they thought they’d get ahead of that,” said one former senior intelligence official close to the deliberations. “They decided it was better to put out a clean set of key judgments.” Vice President Cheney went so far as to say that officials expected to lose control of some classified material. “There was a general belief — that we all shared — that it was important to put it out, that it was not likely to stay classified for long, anyway,” Cheney told The Politico on December 5. “Everything leaks.”

The leak-prevention strategy was a stark departure from the guidelines that McConnell had set out, both in November and a month earlier, when he issued this official policy: “The possibility that the [key judgments] or other positions of an estimate will be leaked is not a sufficient reason for preparing unclassified [key judgments].” In a briefing with reporters after the NIE was released, a senior intelligence official acknowledged that declassification “obviously represents a departure from [McConnell's] guidance.”

The banner headline of the key judgments — “that in fall 2003, Tehran halted its nuclear weapons program” — put the intelligence community precisely where McConnell didn’t want it to be: in the middle of a ferocious political and policy debate in which sources and methods of the intelligence on Iran, as well as the analysis, are being openly discussed, exposed, debated, and, yes, cherry-picked to suit a range of agendas. Indeed, even though the NIE does not say that Iran poses no nuclear threat, the key judgments on areas besides the weapons program have had to compete with the dramatic top-line assessment.

Because the new estimate upends its predecessor, made in 2005, and has undercut any nuclear-related pretext for a U.S. bombing of Iran, the political and ideological dispositions of the analysts who wrote the NIE are, predictably, under scrutiny. Within days of the key judgments’ release, former Bush administration officials and neoconservative icons mounted a full-scale attack on McConnell’s lieutenants, some of whom had long careers in the State Department and have, the critics contend, historically underestimated Iran.

These critics characterized the NIE as the lieutenants’ way of cutting off Cheney and the president on their presumed path to war with Iran — a contention that wasn’t refuted by senior intelligence officials’ repeated assertions that Iran’s decision to stop its program in 2003 and to keep it shuttered resulted directly from international pressures and sanctions. Indeed, intelligence officials have been careful not to assert that the 2003 invasion of Iraq was the key motivator for Iran’s change of plans. Whether McConnell’s aides meant to pre-empt the White House or not, the conclusion is undeniable: The intelligence community is at odds with President Bush’s forceful rhetoric on Iran.

Since the NIE was released, McConnell has been notably absent from the public fracas. His deputy, Donald Kerr, a veteran nuclear weapons expert, has given the intelligence community’s only two on-the-record statements about the estimate. McConnell was out of the country when the key judgments were released.

Around Washington, rumors persist that McConnell threatened to resign over the issue. It’s not clear, however, whether he staked his tenure on the NIE being released or withheld, or whether he saw any cherry-picking by the White House, but the gossip is one more measure of just how political the release of this document has become. Observers point out that in the month preceding the NIE, Bush warned that Iran’s nuclear ambitions could lead to “World War III,” and Cheney, four days later, gave a bellicose speech reminiscent of the run-up to war with Iraq over its weapons programs. The White House already knew by then, at a minimum, that the intelligence community was vetting potentially groundbreaking intelligence on Iran that could change the NIE.

Perhaps under pressure to back up their bold new claims on Iran, senior officials have gone further, giving on-background press interviews in which they catalog the streams of intelligence that led the analysts to change their nuclear conclusions — purloined laptop computers loaded with weapons diagrams; notebooks and intercepted phone calls from high-ranking officials; and, as reported by the Los Angeles Times this week, a clandestine operation called “Brain Drain,” in which the CIA helped mid- and top-level Iranian nuclear experts flee the country.

Unless officials are trying to affect the Iranian government’s actions through a massive disinformation campaign, it would seem that the intelligence community has set aside McConnell’s concerns about sources and methods. “I’m shocked by the level of public discussion,” said a former senior intelligence official who worked on Iranian issues for many years, adding, “I don’t see much good that comes from releasing NIEs.”

Kerr has said that the release “was coordinated in discussion with senior policy makers,” but that the intelligence community “took responsibility for what portions … were to be declassified.” Officials weighed “the importance of the information to open discussions about our national security” against protecting sources and methods, he said, and “felt it was important to release this information to ensure that an accurate presentation is available.”

Still, only a dramatic turn of events would have led McConnell to abandon his policy of not making NIEs public, several former officials who know him said. One former high-ranking official involved in clandestine operations said that in more than 30 years in the intelligence business, he had never seen a key judgment change so dramatically so fast — indicating that the new intelligence that officials picked up amounted to a veritable “smoking gun.”

“Keep in mind, this thing had been built up, which is somewhat unusual for an NIE,” said another former senior official, who has also worked on Capitol Hill. The document was months behind schedule, widely anticipated, and focused on one of the top foreign-policy issues of the moment. “I think this was an extraordinary circumstance,” the former official said.

Expressing concern over the public airing of sources, a Senate staffer said that the NIE “has certainly been sucked into a political debate,” and that McConnell is clearly concerned about the effect that the fallout might have on analysts. “For that, we will have to wait and see,” the aide said. “I still think that he simply had no choice. There was no way this would stay secret, and he didn’t want to be accused of trying to bury it. I think he held his nose and let it go.”

Many intelligence professionals concur. And in the NIE’s release, they see signs not of an outright insurrection against the Bush administration but of a reassertion by the intelligence community of its ability to influence policy — public or otherwise. McConnell’s team is hardly backing down in the face of the neocon onslaught. Last Saturday, Kerr shot back at the NIE’s critics in an unusual and terse public statement. Labeled “In response to those questioning the analytic work and integrity of the United States intelligence community,” Kerr’s statement said that the agencies’ “task … is to produce objective, ground-truth analysis. We feel confident in our analytic tradecraft and resulting analysis in this estimate.”

So there.

Published in National Journal.