THE OFFICE of the assistant to the president for national-security affairs in the West Wing of the White House is a spacious, well-lit corner room in a building where space is at a premium. It contains not only the national-security adviser’s large desk but also a table for lunch discussions and other small meetings as well as a couch and easy chairs for more relaxed discussions. In April 2007, this commodious setting was the scene of a remarkable meeting. Stephen Hadley, the national-security adviser at the time, welcomed Meir Dagan, head of Israel’s Mossad intelligence service, who came with a special briefing for his American host. Dagan revealed a secret nuclear reactor in the final stages of construction in the Syrian desert, developed with the help of North Korea. Knowledge of this project constituted a stunning intelligence coup for Israel.

Later that year, on September 6, 2007, the Israeli Air Force destroyed Syria’s nuclear facility at Al Kibar along the Euphrates River. The mission emerged from more than two decades of comprehensive intelligence collection and analysis by American and Israeli intelligence services targeting Syria’s development of weapons of mass destruction. It was a dramatic demonstration of intelligence success—all the more so given the ongoing civil war that has devastated Syria since 2011. The world does not need to worry about a Syrian nuclear reactor under threat of capture by Islamic radicals. Israel took that concern off the table.

But the incident also demonstrated that once a policy-intelligence feedback loop becomes dysfunctional, as happened to the George W. Bush administration after it exaggerated and distorted intelligence estimates to justify the Iraq War, there are serious policy implications. Israel wanted America to take out the reactor, but Bush was constrained by an intelligence community unwilling to cooperate with another major military operation based primarily on intelligence data.

THE STORY begins in the early 1980s, when the Syrian government began developing weapons of mass destruction. Despite achieving strategic surprise in the Yom Kippur War and foiling Israel’s ambitions to remake Lebanon into an ally in the 1982 Lebanon war, Damascus recognized that it was no match for Israel in a conventional war. The Israel Defense Forces (IDF) marched to the outskirts of Damascus in 1973 and nine years later evicted the Syrians from Beirut and southern Lebanon. Thus, President Hafez al-Assad sought to develop chemical weapons to create a balance of terror between Israel and Syria that would deter Israel from threatening Damascus or trying to oust his regime in any future conflict.

Assad turned to Syria’s preeminent scientific-research establishment to begin developing weapons of mass destruction to threaten Israel’s cities. By the mid-1980s the Centre d’Etude et de Recherche Scientifique (CERS) in Damascus was able to develop a reliable chemical weapon using the nerve agent sarin. Sarin, discovered by four German scientists just before World War II and named as an acronym of their last names, is estimated to be more than five hundred times as toxic as cyanide. CERS scientists were able to produce the nerve agent in significant quantities and achieve a high level of purity to make it lethal.

The Syrians then mated the chemical weapon with a reliable delivery system, the Soviet-built Scud missile, also a weapon of German design. The Russians essentially copied the German V-2 missile after the Second World War and in the 1970s began exporting the system to their Arab allies. Mating a chemical warhead to a missile is not a simple technical challenge, but the Syrians succeeded in doing so in the mid-1980s and successfully carried out tests with the system. Syria also developed chemical bombs that could be dropped by aircraft. Syria was not alone in developing sarin weapons; Iraq did so as well and actually used them extensively, along with other chemicals, on the battlefields of the Iran-Iraq war.

In January 1988, the Sunday Times of London reported on its front page that Israeli officials had informed the paper that Syria had successfully developed the chemical warheads for its Scud missiles and that Israel was considering a preemptive attack to destroy the manufacturing plants. Syria denied that it was making chemical weapons. In the end, Israel chose not to initiate a preemptive strike, probably because the Syrians had developed a sufficient number of manufacturing plants, finished warheads and missiles that an attack likely would fail to eliminate the danger and might provoke a Syrian strike on Tel Aviv.

Syria continued to refine its chemical weapons during the 1990s even as it pursued peace negotiations with the Israelis. In addition to sarin warheads, it also developed the even more toxic nerve agent VX and expanded the number of its missile delivery systems with assistance from North Korea. The American and Israeli intelligence communities monitored the improvement of the Syrian arsenal. In January 2000, the Syrian-Israeli peace process led to a summit in Shepherdstown, West Virginia, that came tantalizingly close to a peace agreement. But it fell just short of culmination. The draft agreement made no mention of Syria’s WMD. Two months later, a final effort to arrange a peace agreement failed at a summit between Assad and President Bill Clinton in Geneva. In June 2000, Assad died and was succeeded by his son Bashar.

Before the elder Assad’s death, he entered into discussions with North Korea on a highly secret program to build a nuclear reactor in western Syria with Pyongyang’s assistance. According to former CIA director Michael Hayden, cooperation between Syria and North Korea on nuclear issues began in the late 1990s, perhaps in 1997. A subsequent review of imagery indicates that construction at Al Kibar began in 2002. According to Hayden, the CIA saw the construction as suspicious but did not recognize it as a nuclear reactor until “a report from a foreign partner initially identified the structure at Al-Kibar as a nuclear reactor similar to one in North Korea.”

THE ISRAELIS tentatively identified the reactor for what it was in late 2006. According to Israeli and German press reports, the Mossad obtained access to the laptop computer of a Syrian government official while he was visiting London in 2006. The laptop contained construction plans, letters and hundreds of photographs of the reactor at various stages in its development since 2002. Most importantly, the photographs of the interior of the site demonstrated it was a nuclear reactor. It is unclear if the Israelis had British cooperation in gaining access to the computer.

The CIA then employed classic “multidisciplinary, blue-collar analysis,” as Hayden put it, to bring together “virtually every form of intelligence—imagery, signals, human source, you name it . . . so that they were never completely dependent on any single channel” of source material. He highlighted the “quality of tradecraft, in terms of collection and analysis, and the value of collaboration . . . with foreign services.”

A six-minute CIA video, released after the reactor’s destruction, indicates the agency analysis demonstrated that the Al Kibar facility was a gas-cooled, graphite-moderated nuclear reactor intended to produce plutonium for nuclear weapons. Al Kibar was a North Korean design, similar to that country’s reactor at Yongbyon. Only North Korea had built reactors of this design in the previous thirty-five years. The CIA reached its conclusions by using satellite imagery, ground photographs of the interior of the facility and a computer-produced graphic image of the reactor. It also photographed North Korean personnel in Syria involved in the construction.

The CIA video concluded that the construction was complete by April 2007, after which the reactor could have gone operational at any time with sufficient fuel. Hayden noted that the American analysts reviewed potential alternative explanations for the facility, but “the arguments simply didn’t add up.” He stressed that the “foreign partnerships . . . were critical to the final outcome” of the analysis. They were “akin to working together on a complex equation over a long period. Each tries to solve a variable that in turn helps a partner solve another, and so on until we’ve cracked the case. That’s what good intelligence is all about.”

The Israelis supplemented their data with soil and plant samples acquired by an IDF commando mission in August 2007. Soldiers from the Sayeret Matkal, the IDF’s elite commando unit, were covertly flown in by CH-53 helicopters to the Al Kibar region to acquire the samples.

This intelligence collection, and the detection of the Syrian nuclear reactor, represented an unqualified intelligence success. American and Israeli covert operations had successfully tracked Syria’s efforts to develop weapons of mass destruction over two decades. But the interaction between intelligence and policy was more complicated, especially on the American side.

Some press accounts of the reactor episode in Israel and elsewhere emphasize a possible Iranian role in the project. Israeli accounts suggest the Syrian project was funded in part or in full by Tehran, and one says Iran provided $2 billion for the project.

But the CIA’s video and Hayden’s public comments don’t mention Iran, and President Bush’s account of his discussions with Prime Minister Ehud Olmert makes no mention of any Iranian role. Nor did Vice President Dick Cheney’s subsequent accounts suggest involvement by Iran. No Israeli government source has claimed an Iranian role in the Syria project, either, and Israeli government officials normally are not hesitant to discuss Iranian nuclear developments. A senior Israeli intelligence officer directly involved in the operation told me that the evidence does not confirm an Iranian role in or even knowledge of the reactor, although it is always difficult to be definitive about funding sources for secret projects.

Israeli accounts also stress the role of General Mohammed Suleiman in the project. Suleiman was in charge of the reactor’s construction and security. An engineering graduate from Damascus University, Suleiman was Assad’s chief adviser on all WMD projects and dealt extensively with the North Koreans and Iranians. Suleiman was assassinated in August 2008 at his seaside home near Tartus, Syria, reportedly by Israeli naval commandos.

Importantly, neither American nor Israeli intelligence located a plutonium-reprocessing facility near Al Kibar or anywhere in Syria. While a nuclear reactor potentially represents the first step toward a nuclear-weapons capability, it alone would not be sufficient to build the weapons. The country would also need a reprocessing facility—a more difficult technical challenge to build—in order to convert the plutonium from the reactor’s spent fuel into a high enough grade for it to be usable in nuclear weapons. Syria also lacked sufficient fuel to start the reactor on its own; it would need a fuel supply from some outside source. That presumably would have been North Korea. The absence of a reprocessing facility suggests the reactor at Al Kibar may have been for supplying North Korea and its nuclear-weapons program more than it was for a Syrian program, at least until Syria built a reprocessing facility. This intriguing absence would raise questions that would have serious implications for the policy community in the United States.

IN MARCH 2007, Israeli prime minister Ehud Olmert set up a small team of experts to advise him and Defense Minister Ehud Barak on what to do about the Syrian threat. The following month, as previously mentioned, Mossad director Meir Dagan came to Washington to see Stephen Hadley to discuss the situation. Dagan brought photographs from his laptop and imagery taken by Israel’s satellites to share with Hadley, who also previously had his own briefing from the CIA. Cheney was present for Dagan’s briefing, which he describes as including satellite imagery and photographs of the North Korean team leaders in Syria.

Bush described the American decision-making process in his memoir. In spring 2007, shortly after the Dagan visit, he was briefed extensively on the Israeli information. “Our strong suspicion was that we had just caught Syria red-handed trying to develop a nuclear weapons capability with North Korean help,” he wrote. Shortly thereafter, Olmert called Bush to request that the United States “bomb the compound.” Bush asked for options from his national-security team and an intelligence assessment from Hayden. The military favored an air strike if force was to be used, while the diplomatic option would be to brief allies on the intelligence and collectively go to the International Atomic Energy Association (IAEA) to demand Syria shut down and dismantle the reactor under IAEA supervision. If Syria refused, then “we would have a clear public rationale for military action.” Secretary of Defense Robert Gates and Secretary of State Condoleezza Rice both favored the diplomatic option. Cheney supported an American military attack.

The intelligence assessment “clarified my decision,” according to Bush. Hayden told the president that intelligence-community analysts “had high confidence that the plant housed a nuclear reactor. But because they could not confirm the location of the facilities necessary to turn the plutonium into a weapon, they had only low confidence of a Syrian nuclear weapons program.” In her memoir, Rice credits the intelligence assessment as critical in convincing her that to bomb the reactor in the “face of uncertain intelligence was, to put it mildly, reckless.” Bush informed Olmert that he had chosen the diplomatic option on the basis of the intelligence analysts’ estimate. “I cannot justify an attack on a sovereign nation unless my intelligence agencies stand up and say it’s a weapons program,” he told Olmert. A diplomatic approach would fully protect Israel’s “interests and your state,” he argued, telling the prime minister that this approach “makes it more likely we can achieve our interests as well.”

Cheney later described the decision-making process as well. He attended the first briefing with Dagan in April 2007. At a national-security principals meeting in the family quarters on the second floor of the White House on June 17, Cheney urged an American military attack on the reactor. He later wrote that Director of National Intelligence Mike McConnell had “high confidence” it was a reactor, but he makes no mention of the second low-confidence judgment. Cheney also describes a second principals meeting in late June, at which the president asked his top advisers for advice. Only Cheney favored an American military strike, while Rice, Hadley and Gates supported a diplomatic response.

“The prime minister was disappointed,” Bush relates. The Israeli leader told the president that a Syrian nuclear-weapons program represented an “existential” issue for Israel. Olmert predicted that diplomacy “would bog down and fail,” and added that the U.S. strategy was “very disturbing to me.” He then ended the conversation.

On September 6, 2007, Israel launched a military strike and destroyed the reactor without any effort to alert the IAEA, the United Nations or the international community. Israel’s decision was consistent with its history. In 1981, Israel used force to destroy Iraq’s nuclear reactor and maintain its own regional nuclear monopoly. It is well known that Israel has its own nuclear arsenal, although it has never acknowledged as much publicly. Every Israeli prime minister since David Ben-Gurion deliberately has taken an evasive posture on the issue, but Israel never has signed the Nuclear Non-Proliferation Treaty.

Ben-Gurion set up the Israeli Atomic Energy Commission in 1952, just four years after the country’s independence, and concluded a deal with France a few years later to secretly build the Dimona nuclear reactor. By 1960 the CIA had uncovered the project and was convinced that “plutonium production for weapons is at least one major purpose of this effort.” President John F. Kennedy tried to persuade Israel to forgo the bomb without success. By 1974 the U.S. intelligence community concluded that Israel had produced and stockpiled a small number of fission weapons, and press reporting about the Israeli program was commonplace.

The Federation of American Scientists’ latest estimate of global nuclear stockpiles pegs the size of Israel’s arsenal today at roughly eighty nuclear weapons, deliverable by aircraft, cruise missiles from Israeli submarines built in Germany or Jericho ballistic missiles. This estimate is consistent with those from other think tanks around the world.

Israel has threatened to use its nuclear arsenal at least once. In 1991, on the eve of the Gulf War, Israel’s then deputy chief of staff Ehud Barak told King Hussein of Jordan to pass a message to Saddam Hussein and Iraq at a secret meeting in England. “If one single chemical warhead falls on Israel, we’ll hit Iraq with everything we have got. . . . Look at your watch and forty minutes later an Iraqi city will be reduced to ashes.” It worked. Saddam fired conventionally armed warheads at Tel Aviv, Haifa and Dimona, but no chemicals.

Given the power of such a threat, it is understandable why Israel would seek to preserve its monopoly on nuclear weapons in the Middle East. The decision to attack and destroy Syria’s reactor was fully consistent with that long-standing but unstated Israeli policy.

THE AMERICAN decision not to attack was more complex. Bush says he was constrained by the analysts’ assessment that, while Al Kibar was clearly a nuclear reactor, they were “less confident” it was part of a Syrian nuclear-weapons program, given the lack of a reprocessing facility.

That decision reflected the state of intelligence-policy interaction in the later stages of the Bush administration. The Iraq War had significantly influenced this interaction. The intelligence community had been heavily criticized in the media and Congress for allegedly allowing the Bush administration to pressure it into exaggerating the Iraqi WMD program to justify the war. Under intense political pressure, Bush created the Commission on the Intelligence Capabilities of the United States Regarding Weapons of Mass Destruction, which reported to the president on March 31, 2005.

The commission concluded that

on the brink of war, and in front of the whole world, the United States government asserted that Saddam Hussein had reconstituted his nuclear weapons program, had biological weapons and mobile biological weapon production facilities, and had stockpiled and was producing chemical weapons. All of this was based on the assessments of the U.S. Intelligence Community. And not one bit of it could be confirmed when the war was over. . . . making this one of the most public—and most damaging—intelligence failures in recent American history.

It was a devastating conclusion. The commission—composed of experienced public servants who had served in both Republican and Democratic administrations—put the burden of blame for analytic and collection shortcomings on the intelligence community. It specifically did not address, and was not authorized to address, the issue of how the policy community used the intelligence it received in 2003. The commission did examine “the possibility that intelligence analysts were pressured by policymakers to change their judgments” to support policy. It said the intelligence analysts “universally agreed” this was not the case, although it also agreed that “it is hard to deny the conclusion that intelligence analysts worked in an environment that did not encourage skepticism” about Iraqi possession of WMD.

Many in and out of the intelligence community sharply and publicly disagreed with the commission’s decision not to pursue aggressively the question of “politicization” of intelligence. Intelligence officers who retired after the war began were among the most critical of the administration. Tyler Drumheller, a twenty-five-year veteran of the clandestine service who rose to European division chief in the CIA’s Directorate of Operations, wrote in 2006 that “never have I seen the manipulation of intelligence that has played out since the second President Bush took office.” Drumheller reported that intelligence suggesting there were no Iraqi WMD was overlooked or ignored in the CIA because of political pressure from the White House, especially from Cheney. He asserts that “the books had been cooked, the bets placed.”

Former director of central intelligence George Tenet was more restrained in his 2007 memoir. Although he conceded the intelligence community had made serious errors in its Iraq WMD estimates, he was less harsh on the Bush policy team. Six former intelligence officers released a letter to Tenet immediately thereafter in which they accused the former director of being “a willing participant in a poorly considered policy to start an unnecessary war. . . . You were well aware that the White House tried to present as fact intelligence you knew was unreliable.” In short, the 2007 environment was toxic with strong accusations from former senior intelligence officers that the Bush team consciously manipulated intelligence to justify policy decisions it had made independent of intelligence estimates.

Whatever the merits of the arguments on either side of this controversy, my purpose here is to probe the impact of the issue. By 2007, the controversy had created a reality in which Bush was constrained by his track record in dealing with intelligence assessments. As he puts it in his memoir, he simply had no option to take military action once the intelligence community said it had “low confidence” of a Syrian nuclear-weapons program. The policy-intelligence interface had become a public issue like never before in American history.

Cheney agreed. He concluded his account of the decision-making process in the Bush White House in 2007 with the judgment that “although the evidence about the nuclear reactor was solid, the intelligence community’s failure on Iraq was still affecting our decision making.” He added, “That experience made some key policymakers very reluctant to consider robust options for dealing with the Syrian plant.”

It can be argued that the outcome was nonetheless positive because Israel, taking the action Bush could or would not take, destroyed the reactor. It seems clear today that ensuring Syria would not possess a nuclear reactor under Assad’s despotism was the right choice, particularly in light of the political and social chaos that subsequently descended upon that country. But for America the story illustrates what happens when the policy-intelligence process breaks down dramatically and publicly. In that circumstance, American policy makers become tightly constrained politically. When policy makers lose the trust of the intelligence community and the public, the consequences are serious.

Bruce Riedel is director of the Intelligence Project at the Brookings Institution. A career CIA officer, he has advised four presidents on Middle East and South Asian issues on the staff of the National Security Council.