The Mossad extracted evidence of the nuclear site from the computer of a Syrian official. Photoillustration by Dan Winters.

In the first days of March, 2007, agents from the Mossad, the Israeli intelligence agency, made a daring raid on the Vienna home of Ibrahim Othman, the head of the Syrian Atomic Energy Commission. Othman was in town attending a meeting of the International Atomic Energy Agency’s board of governors, and had stepped out. In less than an hour, the Mossad operatives swept in, extracted top-secret information from Othman’s computer, and left without a trace.

In recent months, Israel and the United States had become worried by Syria’s nuclear ambitions. In the nineteen-nineties, Syrian President Hafez al-Assad sought to buy nuclear research reactors from Argentina and Russia, but the deals fell through under U.S. pressure. Toward the end of 2006, Israel began to pick up intelligence of possible renewed nuclear activity. There were also suspicions about a large, “enigmatic” building under construction in the desert of northeastern Syria, General Michael Hayden, the director of the C.I.A. at the time, told me.

The information the Mossad operatives recovered was damning: roughly three dozen color photographs taken from inside the Syrian building, indicating that it was a top-secret plutonium nuclear reactor. The reactor, called Al Kibar, was nine hundred yards from the Euphrates River and halfway between the borders with Turkey and Iraq. The photographs showed workers from North Korea at the site, which was far from Syria’s biggest cities. The sole purpose of this kind of plutonium reactor, in the Mossad’s analysis, was to produce an atomic bomb. Inside, the reactor had many of the same engineering elements as the North Korean reactor in Yongbyon—a model that no one but the North Koreans had built in the past thirty-five years.

Two and a half decades earlier, Israel had dispatched bombers to Iraq to destroy the Osirak nuclear reactor. That strike marked the rise of the Begin doctrine, named for Israeli Prime Minister Menachem Begin, which held that no Israeli adversary in the Middle East should be allowed to acquire a nuclear weapon. Israel itself has reportedly possessed nuclear weapons since roughly 1967, although it has never either admitted or denied it; the London-based International Institute for Strategic Studies estimates that today Israel has as many as two hundred nuclear warheads. Off the record, Israeli officials reject any claim of moral equivalence between their reputed possession of nuclear weapons and Syria’s. One reason, officials say, is Syria’s relationship with Hezbollah and Hamas, both of which are considered terrorist organizations by the U.S. State Department.

On March 8th, days after the raid, Meir Dagan, the director of the Mossad, and two senior officials met with Israeli Prime Minister Ehud Olmert and presented the findings from the raid. During a courtroom appearance last year, at which Olmert was facing corruption charges (he was largely acquitted), he never directly mentioned Dagan or the Syrian site, but he referred obliquely to “a piece of information” that had been put on his desk “such as rarely happens in the country.” He added, “I knew from that moment, nothing would be the same again. The weight of this thing, at the existential level, was of an unprecedented scale.” Olmert pledged to destroy the reactor as soon as possible; if it went “hot,” radiation from its destruction could contaminate the Euphrates.

Five years later, the Al Kibar affair is still not discussed on the record in Israel. When referred to by journalists or military analysts, reports are usually credited to foreign sources. Word has gradually leaked out that Israel destroyed the Al Kibar reactor. Some of the details of the operation have been published. In April, 2008, after several months of secrecy, U.S. intelligence officials finally briefed Congress on their evaluation of the reactor. The most senior members of the Bush Administration, including Bush himself, mentioned in their memoirs how the U.S. responded to the evidence on the reactor. In recent months, I have spoken with about two dozen Israeli and American officials who were knowledgeable about the fate of Al Kibar, to learn exactly what happened and why details of the affair have remained so closely guarded. As Prime Minister Benjamin Netanyahu and his government consider how to confront Iran’s nascent nuclear program, Israel’s response to Al Kibar has emerged as both an exemplary and a cautionary tale.

The small suite of offices where Prime Minister Olmert and a half dozen of his aides worked, in a nondescript government office building in Jerusalem, sits behind glass doors and was so closely watched that it was nicknamed the Aquarium. For that reason, in the days after the discovery of the Syrian installation, Olmert began hosting important meetings at his official residence, on Balfour Street, a couple of miles away.

Olmert, a former cabinet minister and onetime mayor of Jerusalem, had come to power in early 2006 on a platform of peace, and the war that summer with Hezbollah, in Lebanon, had been disastrous for his popularity. In December, in an attempt to restore his focus on peacemaking, Olmert had begun holding regular meetings with Mahmoud Abbas, the President of the Palestinian Authority, to address the establishment of a Palestinian state. On February 15, 2007, a few weeks before the Mossad raid in Vienna, Olmert met with Turkish Prime Minister Recep Tayyip Erdogan, in Ankara, and asked him to explore whether Syrian President Bashar al-Assad—the son of Hafez—would be willing to open secret peace talks with Israel. After meeting with Assad on April 3rd, Erdogan reported back to Olmert that Assad was willing. By that time, Israel had discovered evidence of the Syrian reactor, and a grim resolve had set in.

The briefings on Balfour Street began with Israel’s former Prime Ministers, including Shimon Peres, Ehud Barak, and Netanyahu, Olmert’s political rival. The leaders were summoned one by one, to insure confidentiality and to prevent leaks. A second group—including Amir Peretz, the Defense Minister; Gabi Ashkenazi, the Israel Defense Force’s chief of staff; Amos Yadlin, the I.D.F. head of military intelligence; Yuval Diskin, the head of the Shin Bet, Israel’s security service; and Dagan, of the Mossad—met most Fridays from late March of 2007 through early September. Each member signed a secrecy agreement.

The time came to inform the Americans. On April 18th, during a routine visit to Israel, Robert Gates, George W. Bush’s Secretary of Defense, met with his Israeli counterpart, Peretz. Because Peretz does not speak English fluently, an index card was prepared for him, which he could refer to as he divulged the news about the reactor. Olmert also dispatched Dagan, along with two of Olmert’s top personal aides, Yoram Turbowicz and Shalom Turgemen—nicknamed TnT by U.S. officials—to Washington, to report the news to other senior U.S. officials. Dagan briefed his U.S. counterpart, Hayden, the C.I.A. director. Dagan, Turbowicz, and Turgemen met with Vice-President Dick Cheney and the national-security adviser, Steve Hadley. Dagan presented them with the photographs of the site and other information. According to one former senior U.S. official, Cheney, who had been urging the intelligence community to investigate a link between North Korea and Syria, was vindicated by the news.

President Bush instructed his intelligence chiefs to verify the Israeli claims; the disastrous intelligence failure on weapons of mass destruction in Iraq was fresh in everyone’s mind. Bush’s words, according to the former U.S. senior official, were “Gotta be secret, and gotta be sure.” A C.I.A. crisis task force was established, and, according to the same official, the C.I.A. compared “handheld” photographs of the site with “overheads” taken by American satellites. The photographs were then given to the National Geospatial-Intelligence Agency, which analyzes imagery and map-based intelligence for policymakers and the national-security community. The N.G.A. determined that the two sets of photographs were valid, as did nuclear experts at the Department of Energy and an outside nuclear-proliferation authority. Finally, an ad-hoc C.I.A. “red team” concluded, according to the former senior U.S. official, “If it’s not a nuclear reactor, then it’s a fake nuclear reactor.”