As the civil war in Syria enters its third year, there is much discussion of the regime’s chemical weapons and whether Syria’s Bashar al-Assad will unleash them against Syrian rebels, or whether a power vacuum after Assad’s fall might make those horrific tools available to the highest bidder. The conversation centers on Syria’s chemical weaponry, not on something vastly more serious: its nuclear weaponry. It well might have. This is the inside story of why it does not.

Relations between the United States and Israel had grown rocky after Israel’s incursion into Lebanon in 2006, for Secretary of State Condoleezza Rice believed the Israelis had mishandled both the military and the diplomatic sides of the conflict. While Prime Minister Ehud Olmert’s personal relations with President George W. Bush were excellent, those with Rice were sometimes confrontational—especially when Rice worked at the United Nations to bring the war to a close while Olmert sought more time to attack Hezbollah. Olmert always seemed to ask for 10 days more, while Rice believed the war was not going well and that more time was unlikely to turn the tables.

By the war’s end on August 14, 2006, Olmert’s political status had been diminished and his ability to negotiate any sort of peace agreement with the Palestinians was in doubt. The autumn of 2006 and winter of 2007 saw no movement on the Israeli-Palestinian front, and all the Israeli analysts we consulted said there would be none. We were stuck. And there was another surprise in store.

In the middle of May 2007, we received an urgent request to receive Mossad chief Meir Dagan at the White House. Olmert asked that he be allowed to show some material to Bush personally. We headed that off with a suggestion that he first reveal whatever he had to National Security Adviser Stephen Hadley and to me; I was then the deputy national-security adviser in charge of the Middle East portfolio on the National Security Council. Vice President Dick Cheney joined us in Hadley’s office for Dagan’s presentation. What Dagan had was astonishing and explosive: He showed us intelligence demonstrating that Syria was constructing a nuclear reactor whose design was supplied by North Korea, and doing so with North Korean technical assistance. Dagan left us with one stark message: All Israeli policymakers who saw the evidence agreed that the reactor had to go away.

There then began a four-month process of extremely close cooperation with Israel about the reactor, called al-Kibar. As soon as our own intelligence had confirmed the Israeli information and we all agreed on what we were dealing with, Hadley established a process for gathering further information, considering our options, and sharing our thinking with Israel. This process was run entirely out of the White House, with extremely limited participation to maintain secrecy. The effort at secrecy succeeded and there were no leaks—an amazing feat in Washington, especially when the information being held so tightly was as startling and sexy as this.

Initially, there were doubts that Bashar al-Assad could be so stupid as to try this stunt of building a nuclear reactor with North Korean help. Did he really think he would get away with it—that Israel would permit it? But he nearly did; had the reactor been activated, striking it militarily could have strewn radioactive material into the wind and into the nearby Euphrates River, which was the reactor’s source of water needed for cooling. When we found out about the reactor, it was at an advanced construction stage, just a few months from being “hot.”

The consideration of what to do about the reactor continued alongside tense meetings between Rice and Israel on how to proceed with the Palestinians, but the two initiatives did not collide. For the most part, this was because different people were involved. Military and intelligence personnel uninvolved in peace negotiations were the key interlocutors for Israel in considering the al-Kibar reactor, as were individuals on the vice president’s staff who were sympathetic to Israel’s position. The work on al-Kibar was a model both of U.S.-Israel collaboration and of interagency cooperation without leaks. Papers I circulated to the group were returned to me when meetings ended or were kept under lock and key; secretaries and executive assistants were kept out of the loop; meetings were called under vague names such as “the study group.”

The debates were vigorous in our secret meetings in the White House Situation Room. The role of those in the Situation Room was not to decide what was to be done about the reactor; it was merely to be sure every issue had been thoroughly debated and was covered in the memos we drafted for the administration’s principal officials on foreign-policy matters and for the president. This was an excellent example of how policy should be made. Several times, principals—Rice and Hadley, Defense Secretary Robert Gates, CIA Director Michael Hayden, Director of National Intelligence Mike McConnell, Joint Chiefs of Staff Chairman Peter Pace and Vice President Cheney—trooped over to the president’s living room in the residence section of the White House to have it out before him, answer his questions, and see what additional information he sought.

I attended all these meetings as note taker, and the notes are under lock and key at the National Archives.

The day I left those notes on the floor under my chair in the president’s living room, and discovered when back at the NSC that I no longer had them, remains emblazoned in my mind. These were among the most sensitive notes then existing in the U.S. government, amazing precautions for secrecy had been taken, and I had simply left them on the floor. Pale and drenched with sweat, I ran back to the residence, where the butler graciously let me back in and accompanied me to the Yellow Oval Room where we had met. There was my portfolio, under the chair, untouched. Well, I thought, if the butler keeps his mouth shut, I may actually not be shot after all.

The facts about al-Kibar were soon clear, and about those facts there was no debate: It was a nuclear reactor that was almost an exact copy of the Yongbyon reactor in North Korea, and North Koreans had been involved with Syria’s development of the site. Given its location and its lack of connection to any electrical grid, this reactor was part of a nuclear-weapons program rather than intended to produce electric power.

The array of options was clear as well: overt or covert, Israel or United States, military or diplomatic. The United States and Israel both had an obvious military option: Bomb the site and destroy the reactor. This was not much of a military challenge, General Pace assured the president. Whether anything short of a military strike could destroy the reactor was another question, and the difficulties with such an option were obvious: Just how would you get the needed explosives to the site except through a military attack? It was soon agreed that a covert option did not exist, and military options were quickly designed to make the reactor disappear; as Dagan had said when he first visited us, the Israelis clearly believed it had to go away. We developed elaborate scenarios for U.S. and Israeli military action addressing these issues: Whom would you inform when, what would you announce and what would you keep secret, and what if anything would you say to the Syrians?

But a diplomatic option existed as well, and we did draw up elaborate scenarios for it. We would begin by informing the International Atomic Energy Agency (IAEA) of the facts and making them public in a dramatic session before the IAEA Board of Governors in Vienna. We would demand immediate inspections and that Syria halt work on the reactor. If Syria refused, we would go to the UN Security Council and demand action. If there was no action, the military option in theory remained open.

However, this diplomatic option seemed faintly ridiculous to me. For one thing, it would never be acceptable to Israel, whose experience with the United Nations was uniformly bad. The Jewish state would never trust its national security to the UN. For another, it would not work; Syria’s friends in the UN, especially Russia, would protect it. At the IAEA, we had plenty of experience with Director General Mohamed ElBaradei, an Egyptian. He was redefining the director general’s role from that of inspector and cop to that of peacemaker and diplomat; he would seek a deal with Syria rather than concerted action against it. Moreover, taking the reactor issue to the UN and the IAEA meant handing it over to the State Department, and I thought an issue of this importance should be handled in the White House.

Finally, the argument that there would always remain a military option as a last resort was misleading at best. Once we made public our knowledge of the site, Syria could put a kindergarten right next to it or take some similar move using human shields. Military action required secrecy, and once we made any kind of public statement about al-Kibar, that option would be gone.

The vice president thought the United States should bomb the site. Given our troubles in Iraq and the growing confrontation with Iran, this would be a useful assertion of power and would help restore our credibility. As he later wrote:

I again made the case for U.S. military action against the reactor. Not only would it make the region and the world safer, but it would also demonstrate our seriousness with respect to non-proliferation….But I was the lone voice. After I finished, the president asked, “Does anyone here agree with the vice president?” Not a single hand went up around the room.

My hand did not go up (and as we left the president’s living room that day, June 17, I apologized to the vice president for leaving him isolated) because I thought the Israelis should bomb the reactor, restoring their credibility after the annus horribilis of 2006 with the Second Lebanon War and then the 2007 Hamas takeover of Gaza. It seemed to me that Israel would suffer if we bombed it, because analysts would point out that Israel had acted against the Osirak reactor in Iraq in 1981 but had become paralyzed when it came to Syria. Such an analysis might embolden Iran and Hamas, a development that would be greatly against American interests. Moreover, hostile reactions in the Islamic world against the bombing strike might hurt us at a time when we were fighting in Afghanistan and Iraq—another argument for letting Israel do the job. (I did not think there would be any such reactions, but this was an argument worth deploying in our internal debate.)

Secretaries Gates and Rice argued strenuously for the diplomatic option. Gates also argued for preventing Israel from bombing the reactor and urged putting the whole relationship between the United States and Israel on the line. His language recalled the “agonizing reappraisal” of relations Eisenhower’s secretary of state, John Foster Dulles, had threatened for Europe in 1953 if the Europeans failed to take certain defense measures: They simply had to do what we demanded or there would be hell to pay.

I thought I understood why Gates did not want the United States to bomb Syria: America was a steward of wars in two Islamic countries already, so striking a third one seemed terribly unattractive to him. Why he was almost equally insistent that we prevent Israel from bombing it was never comprehensible to me, nor was Rice’s similar position. It seemed clear to me that if we could not prevent Syria from undertaking a nuclear-weapons program, our entire position in the Middle East would be weakened, just as it was being weakened by our inability to stop the Iranian program. If there were too many risks and potential complications from striking Syria ourselves, we should not only allow but encourage Israel to do it; a Syrian nuclear program in addition to Iran’s should be flatly unacceptable to the United States.

I tried to think my way through Rice’s reasoning, but came up with only one theory. She had simultaneously been expressing opposition to a new program of increased military aid to Israel. This indicated to me that she had an underlying strategy: She did not want Israel feeling stronger. Rather, she wanted Israel, and especially Prime Minister Olmert, to feel more dependent on the United States. That way she would be able to push forward with plans for an international conference on Israeli-Palestinian issues and for final-status talks leading to the creation of a Palestinian state before the end of the second Bush term.

I hoped this was not her intention, because it seemed to me that such designs were sure to fail. An Israel that was facing Hamas in Gaza and now two hostile nuclear programs, in Iran and just across the border in Syria, would never take the risks she was asking it to take. I thought we had learned that lesson with Ariel Sharon as Bill Clinton had learned it with Yitzhak Rabin: Wrap your arms around Israel if you want it to take more risks, so it feels more secure, not less.

The arguments for going to the IAEA and UN seemed so flimsy to me, despite the length and detail of the planning memos and scenarios to which they gave rise, that I did not much worry about them. Who could believe these organizations would act effectively? Who could believe we would not be sitting there five years later entangled in the same diplomatic dance over the Syrian program that we were in with respect to Iran?

In the end, our near-perfect policy process produced the wrong result. At a final session in the gracious Yellow Oval Room at the Residence, Bush came down on Rice’s side. We would go to Vienna, to the IAEA; he would call Olmert and tell him what the decision was. I was astounded and realized I had underestimated Rice’s influence even after all this time. The president had gone with Condi.

I tried to figure this one out and could not. Perhaps it was the same worry that Gates had about making another American military strike in the Islamic world. But that would not explain why he bought the IAEA/UN strategy lock, stock, and barrel; instead, he could have said, “Let the Israelis do what they want; let’s just tell them we will not do it.” Years later I asked him if he thought he had been wrong; he said no. It was then, and is still, baffling. In his memoir, Bush explains one key consideration: The CIA told him it had “high confidence” that the facility in Syria was a nuclear reactor but “low confidence” that Syria had a nuclear-weapons program, because it could not locate the other components of the program. The president thought that the “low confidence” judgment would leak, as it surely would have, and the United States would have been attacked for conducting the bombing raid despite the “low confidence” report. That is a reasonable argument, but it explains only why we did not bomb—it does not explain why he urged the Israelis not to do so.

On July 10, I gave Hadley a memo explaining my views on where we stood with the Israelis. First, we were on the verge of telling the Israelis that we had considered which of us should act against the reactor and had decided that neither of us should use force. Moreover, we were going to say we would pressure them not to do so even if they disagreed. And we would be saying all this after Hamas had just taken over Gaza (which it did, in a coup against the Palestinian Authority, in June 2007). Hezbollah was back fully rearmed in Lebanon despite all those UN Security Council resolutions we had told the Israelis would work. Iran was moving toward nuclear capability. Syria was building a reactor that could only be part of a nuclear-weapons program.

It also looked as if we would be telling them we were about to call for an international meeting on the Palestinians that Israelis did not want and that they feared—and would be doing so in a presidential speech that talked about negotiations for Palestinian statehood “soon” (the word was in the speech drafts). Such a big international conference was the State Department’s answer to unsticking a “peace process” that was stuck.

The editorial comment from our friends on the right, I told Hadley, will be that we have taken leave of our senses: Hamas takes over Gaza, Syria and Iran build nukes, and we are handing things over to the UN and then pushing final-status talks? I still did not think there was a need for any presidential speech, but if there were to be one, I wrote that it should be sober about the situation and supportive of the new Palestinian prime minister, Salam Fayyad.

At that point, Fayyad had been prime minister for about a month, and already the PA was changing. It now had a serious, talented, incorruptible executive at the top of the government. This had never been tried before. The least we could do was to back him, firmly and fully, and not spend all our political capital on great conferences. It was, as I recall it, a terrific memo, yet like all the wonderful memos about the Syrian reactor, it had no impact whatsoever. On July 16, the speech that Condi had sought was given. “Bush Calls for Middle East Peace Conference,” the headlines read.

Three days earlier, on July 13, President Bush had called Prime Minister Olmert from his desk in the Oval Office and explained his view. I have gone over this in great detail, Bush explained on the secure phone to the Israeli prime minister, looking at every possible scenario and its likely aftermath. We have looked at overt and covert options, and I have made a decision. We are not going to take the military path; we are instead going to the UN. Bush recounts in his memoir that he told Olmert, “I cannot justify an attack on a sovereign nation unless my intelligence agencies stand up and say it’s a weapons program” and that “I had decided on the diplomatic option backed by the threat of force.” We will announce this approach soon, Bush said on the secure line, and we will then launch a major diplomatic campaign, starting at the IAEA and then the UN Security Council. And of course a military option always remains available down the line.

I wondered how Olmert would react and believed I could predict his response: He would say, “Wait, give me some time to think about this, to consult my team, to reflect, and I will call you tomorrow.” I was quite wrong. He reacted immediately and forcefully. George, he said, this leaves me surprised and disappointed. And I cannot accept it. We told you from the first day, when Dagan came to Washington, and I’ve told you since then whenever we discussed it, that the reactor had to go away. Israel cannot live with a Syrian nuclear reactor; we will not accept it. It would change the entire region and our national security cannot accept it. You are telling me you will not act; so, we will act. The timing is another matter, and we will not do anything precipitous.

This is not the account President Bush gives in his memoir, in which he writes that Olmert initially said, “George, I’m asking you to bomb the compound.” Someday transcripts of their conversation will be available, but Bush’s recollection does not comport with mine.

After that conversation, there was a nearly two-month gap, from July 13 to September 6. We now know the time was filled with Israeli military calculations—watching the weather and Syrian movements on the ground—with the aim of being sure that Israel could act before the reactor went “critical” or “hot.” We knew the Israelis would strike sooner or later. They acted, in the end, when a leak about the reactor’s existence was imminent and Syria might then have gotten notice that Israel knew of its existence. That would have given Assad time to put civilians or nuclear fuel near the site. The Israelis did not seek, nor did they get, a green or red light from us. Nor did they announce their timing in advance; they told us as they were blowing up the site. Olmert called the president on September 6 with the news.

As I had sat in the Oval Office on July 13, listening to his conversation with Olmert, I had wondered how the president would react to the Israeli action. With anger? Or more pressure? None of it. He heard Olmert out calmly and acknowledged that Israel had a right to protect its national security. After hanging up, the president said something like “that guy has guts,” in an admiring tone. The incident was over; the differences over al-Kibar would obviously not affect Bush’s relationship with Olmert or his view of Israel.

So quickly did he accept the Olmert decision that I wondered then, and do still, if the president did not at some level anticipate and desire this result. He had sided with Condi and shown that she was still in charge of Middle East policy, but her “take it to the UN” plan had been blown up along with the reactor. He did not seem very regretful. What is more, he instructed us all to abandon the diplomatic plans and maintain absolute silence, ensuring that Israel could carry out its plan.

The Israeli assessment of Syria’s likely reaction was correct. The Israelis believed that if they and we spoke about the strike, Assad might be forced to react to this humiliation by trying to attack Israel. If, however, we all shut up, he might do nothing—nothing at all. He might try to hide the fact that anything had happened. And with every day that passed, the possibility that he would acknowledge the event and fight back diminished. That had been the Israeli theory, and the Israelis knew their man. We maintained silence and so did Israel—no leaks. As the weeks went by, the chances of an Israeli-Syrian confrontation grew slim and then disappeared. Syria has never admitted that there was a reactor at the site. Soon after the bombing, the Syrians bulldozed the reactor site, but the only way they could be sure their lies about it were not contradicted was to prevent a full examination. When a 2008 site visit by IAEA inspectors found some uranium traces, Syria made sure never to permit a return visit.

Two final points are worth noting. First, in May 2008, Turkish-mediated peace talks between Israel and Syria were publicly announced in Istanbul. The discussions had begun secretly in February 2007, and obviously had continued after the Israeli strike on al-Kibar. It would appear that the strike on al-Kibar made the Syrians more, not less, desirous of talking to the Israelis because it made them afraid of Israeli power. It also made them more afraid of American power until we undermined our own position, which is the second point.

A very well-placed Arab diplomat later told us that the strike had left Assad deeply worried as to what was coming next. He had turned Syria into the main transit route for jihadis going to Iraq to kill American soldiers. From Libya or Indonesia, Pakistan or Egypt, they would fly to Damascus International Airport and be shepherded into Iraq. Assad was afraid that on the heels of the Israeli strike would come American action to punish him for all this involvement. But just weeks later, Assad received his invitation to send a Syrian delegation to that big international confab of Condi’s, the Annapolis Conference, and according to the Arab envoy, Assad relaxed immediately; he knew he would be OK. I had not wanted Syria invited to Annapolis because of its involvement in killing Americans in Iraq, but Condi had wanted complete Arab representation as a sign that comprehensive peace might be possible. It was only years later that I learned that Assad had instead interpreted the invitation just as I had: as a sign that the United States would not seriously threaten or punish him for what Syria was doing in Iraq.

Since the day the Israelis struck the Syrian reactor in September 2007, much has changed in the neighborhood: Assad faces a civil war he cannot win, the “Arab Spring” has replaced Hosni Mubarak with a Muslim Brotherhood government in Egypt, and Israel has now fought two wars with the Hamas statelet in Gaza, in December 2008/January 2009 and in November 2012. Yet there are three lessons from this incident that still bear noting.

First, good “process” and good policy are related but distinct. In the end what counts is output, not input: the foreign policy we adopt, not the proposals that are advanced. And that output depends, when it comes to foreign policy, mostly on one man: the president. That’s the second lesson. Advisers advise; the president decides. All the books about how rival bureaucracies or powerful lobbies determine policy are off the mark; the simpler and truer conclusion is that at any given moment our foreign policy reflects the views of the president.

Finally, this incident is a reminder that there is no substitute for military strength and the will to use it. Think of how much more dangerous to the entire region the Syrian civil war would be today if Assad had a nuclear reactor, and even perhaps nuclear weapons, in hand. Israel was right to bomb that reactor before construction was completed, and President Bush was right to support its decision to do so. Israel was also right in rejecting fears that the incident would lead to a larger war and in believing that it, and the United States, would be better off after this assertion of leadership and determination. That lesson must be on the minds of Israeli, and American, leaders in 2013.