As in other operations by the Mossad, this one – in late 2006 – also began when Unit 8200, the IDF’s Signal Intelligence unit, incidentally intercepted a phone conversation and an electronic reservation a senior Syrian official in Damascus had made in a London hotel.

According to various reports, Israeli and US agencies had tapped the Syrian official’s communication lines since 2002. He had cultivated contacts over the years with North Korea, and his numerous trips to Pyongyang had attracted the attention of the CIA and Mossad.

At this stage though, the existence of a Syrian nuclear program was based simply on speculation and mainly on a number of phone calls between North Korea and a place in northeastern Syria called al-Kibar intercepted by the US National Security Agency (NSA).

While antennas at Unit 8200’s base north of Tel Aviv received the Syrian official’s reservation, a group of young agents sitting not far away at Mossad headquarters were busy discussing the Second Lebanon War.

Similar to the rest of the Israeli defense establishment, the Mossad was not immune to public criticism after the war. For two years, Mossad agents had carried out dozens of secret missions and had risked their lives to collect information about Iran and its proxies scattered across the Middle East. They had paid particular attention to the smuggling routes Iran used for its nuclear project and scrutinized the smallest clues related to the Iranian Revolutionary Guard Corps’ activities in Lebanon, Syria, and elsewhere.

Some of this information enabled the Israel Air Force to destroy Hezbollah’s long-range missile arsenal on the first night of the Second Lebanon War in 2006. Nevertheless, the intelligence achievements and successful covert operations could not prevent the agents at Mossad headquarters from castigating themselves.

The young men and women in the espionage agency were part of the Mossad’s Caesarea Branch, known for its covert operations overseas. Despite the months that had passed, they were still frustrated for having been “frozen” during the war. All of the men had served in combat units; almost all of them had undergone arduous training. But during the war, the Mossad did not let them enlist with the reserves. “You are too valuable,” explained the head of the department, himself a graduate of an elite IDF unit. “Besides, think about if you were needed for an immediate operation here.”

The war was still on everyone’s mind, and the decision makers were preoccupied with public relations aimed at saving Prime Minister Olmert’s image and with approving operational plans for the army. They pushed the Mossad aside.

The call that came through on the red secure phone startled everyone in the room. On the line was the head of the department, who updated them about the Syrian official’s trip to London. The agents were familiar with the protocol in these situations and immediately set preparations to put a new operation into motion.

Two days later, after studying the Syrian official’s facial features and the layout of the prestigious London hotel where he was supposed to be staying, the agents split up and boarded various planes to different destinations. They would rendezvous at the European capital and wait for their target at the airport and the hotel.

During their last briefing before leaving on the mission, their instructions had strongly emphasized gaining access to the official’s laptop or, to be more exact, the information it contained. Two days after arriving at the hotel, the intelligence operatives had reportedly succeeded in installing a Trojan horse on the computer and gleaning all of its contents.

The hard drive contained construction plans, letters, and hundreds of photos that showed the al-Kibar complex at various stages of its development. In photos from 2002 the construction site resembled a tree house on stilts, complete with suspicious-looking pipes leading to a pumping station at the Euphrates. Later photos showed concrete piers and roofs, which apparently were meant to make the building look inconspicuous from above or as if a shoebox had been placed over the structure to conceal it.

The pictures of the facility’s interior, however, left no room for doubt. The Syrians had built a nuclear reactor.

Despite the signs and speculations during the two years preceding the Mossad’s operation, the agents still found this evidence shocking. No one in Israel’s intelligence establishment had imagined that Syrian president Bashar Assad, who had succeeded his father seven years earlier, had decided to break all known taboos and defy all intelligence assessments to develop a nuclear bomb. Most startling was the advanced stage at which Syria’s program was discovered.

The intelligence community also was taken aback by the discovery that Iran was involved and had provided funding and support so that Syria could build a reactor right across the border from Israel and at a time when the future of Iran’s own nuclear program was so unclear. Officials in the CIA, the Mossad, and the IDF’s Aman scoured old files, searching for clues that they might have overlooked and categorized as insignificant but could now help piece together the Syrian nuclear puzzle.

It was possibly the biggest intelligence discovery since the beginning of the decade.

WESTERN INTELLIGENCE agencies had reportedly uncovered the first evidence of a connection between Syria, Iran, and North Korea at Hafez al-Assad’s funeral in June 2000. An entourage accompanying the funeral procession had included top Iranian and North Korean officials. Pictures from the funeral had aroused the suspicions of the Mossad’s nonconventional weapons investigators.

Any link found between North Korea and Iran was always a point of concern, so the Mossad, then under the command of Efraim Halevy, had classified the information that the investigators had collected as top priority.

But the meeting of these heads of state at the funeral appeared to be a one-time incident. Nothing seemed more preposterous at the time than the North Koreans and the Syrians cooperating on the development of such nonconventional means as nuclear weapons.

In 2006, the sketches and documents that the Mossad agents reportedly succeeded in obtaining from the senior Syrian official’s laptop clearly showed that the reactor project was concealed under a front, that is, a farm used to conduct agricultural experiments. Few in the Syrian government and defense establishment, however, were privy to the true nature of the mysterious al-Kibar complex.

The complex was located near the Turkish border and about 130 kilometers from Iraq, which since 2003 had been under the control of US and Coalition forces. Dir al-Zur, the desert region in northeast Syria where al-Kibar is located, was declared a closed military zone even for most of Syria’s senior commanders.

Syria had invested too much money in the project for incidental or intentional information leaks regarding its planning and execution. The vision of the younger Assad and the IRGC, which had financed the project, was that by the time Israel and the West found out about the project, it would be too late for an attack.

Each of the involved parties had a different guiding interest in the project. The North Koreans wanted to make hundreds of millions of dollars and prove how powerful they were in the international scene. In line with their reputation as shrewd economists, the Iranians wanted to spread their nuclear investment to additional locations in order to deter an Israeli attack and, at the same time, establish a reserve facility in case their deterrence did not succeed.

According to assessments made after the reactor was bombed, Iran had spent close to $2 billion on the entire project by bringing the North Korean technology to Syria and purchasing additional components for operating the reactor.

Iran loaned some of the money to Syria, though Assad could never repay the debt. During Ahmadinejad’s visit to Syria in 2006, he guaranteed the money.

But the Syrians themselves had the greatest interest in the project, given that it was in their country. Assad built the reactor in spite of Operation Opera, the Israeli operation in 1981 that destroyed a nuclear reactor in Iraq.

Assad’s decision must have been made hastily and without prior serious indepth discussions regarding Israeli intelligence capabilities and the Israeli response once it learned of the reactor. In the eyes of Syria’s supreme ruler though, creating additional deterrence against Israel was a way to strengthen his standing in the Arab world, to position himself as a world leader, and maybe even to force Israel to return the entire Golan Heights. For him, nuclear weapons were not only about military might but also about taking Syria from the backbenches of the region to the forefront of the world.

In mid-2007, Prime Minister Ehud Olmert contacted President George W. Bush directly in an effort to impress upon the US that the Israelis’ assessment was that the pictures showed a nuclear reactor on the verge of becoming operational. Washington, however, was slightly skeptical and wanted to study the material further.

In their discussions, Olmert told Bush that as far as Israel was concerned the reactor “needed to disappear.” Bush did not dismiss this option, but the professional ranks in his office explained to the Israelis that before doing so three basic questions needed to be answered:

1. What is the real purpose of the facility in the pictures?

2. In what stage is the nuclear program?

3. What can be done to stop Syria from going nuclear?

These questions brought about a period of collaboration that continued up until the week of the attack itself. “The relationship between Israel and the United States peaked then,” a former top Bush administration official said in an interview. “There was unprecedented sharing of intelligence and the dialogue reached an unbelievable level of intimacy.”

In the meantime, to answer these questions, the Mossad and Aman ramped up their intelligence-gathering efforts. They thoroughly interrogated people suspected of having knowledge of the Syrian program, and every piece of information justified a new round of investigation.

People from the Israeli defense establishment began working according to a timeline, trying to discover the so-called point of no return for the nuclear program, or when it would be too late to attack. According to former defense minister Amir Peretz, if the reactor were allowed to go online, they would have to reconsider whether to take military action.

Therefore, in his mind, the attack had to occur before that happened. Olmert and Peretz invited a small number of military specialists and scientists to discuss the potential consequences of both bombing the reactor and ignoring the project.

ONE OF the participants was retired Maj. Gen. David Ivry, who in 1981 was the IAF commander during Operation Opera’s attack on the Iraqi reactor. The arguments for and against a similar strike, as well as about the operational issues, were the same ones they had addressed almost three decades earlier. Among the meeting’s participants were those who claimed that Bashar Assad had built the reactor only in order to impress other Arab countries. They claimed that he had no intention of taking the reactor to the stage where it would present an existential threat to Israel. The overwhelming majority thought otherwise.

In their opinion, Israel’s implicit or quiet acceptance of a nuclear reactor in a Muslim-majority country in the region (as had happened in the Iranians’ case, when it first began exploring nuclear power) would start a nuclear arms race among other Arab countries, even the moderate ones.

Olmert was determined to attack, mainly to rebuild the deterrence threat that had been crushed during the Second Lebanon War and maybe to prove to himself and to the Israeli people what he was really made of. According to a senior US government official, the meetings between Bush and Olmert ended with a mutual understanding: the reactor posed an “existential threat” to Israel, a threat that therefore justified a military attack.

After weeks of discussions and debates in the administration, Bush contacted Olmert and shared his plan for dealing with the reactor.

According to the senior US government official, Bush told the Israeli prime minister that in his opinion the ideal solution was first to approach the International Atomic Energy Agency (IAEA), headed by the Egyptian Mohamed Mustafa ElBaradei. In the event that the IAEA did not help, they could take the evidence to the UN Security Council and ask for sanctions against Syria. If that option failed, then and only then would the United States contemplate a military option.

Olmert, whom fellow Israelis perceived as a political dove without any backbone, came out of these meetings looking as if he knew how to hold his own. He completely dismissed the American plan. Israel had had a bad experience with ElBaradei, who systematically had chosen to overlook Iran’s mounting nuclear violations. In the IAEA’s opinion, Iran was simply a law-abiding country whose goals and tactics were all part of a legitimate political game. Moreover, in Israel’s view, sanctions were not a reliable tool. In 2007, when Bush spoke about future sanctions against Syria, the Israelis already knew that within a short period of time the Syrian reactor would become active.

“Allow me to remind you,” Olmert told the president (according to a senior official in the Bush administration), “that at the beginning of these talks, when I presented the intelligence material to you, I said all along that the reactor needs to go away. If we reveal the data to the UN, the Syrians will build a proverbial kindergarten on top of it and prevent a strike forever.” According to the same source, at this point Olmert realized that the United States was not going to attack the Syrian reactor. Had he looked closer, though, Olmert would have seen the evidence much sooner.

THREE YEARS earlier, during the Sudanese massacre in Darfur, human rights groups had pressured the American administration to take military action to prevent the genocide there. Bush had heard the calls and searched for a viable solution. For him it presented a classical scenario of the forces of good fighting the forces of evil to prevent the murder of the weak and oppressed. The military command suggested attacking the Sudanese Air Force to relay a clear message: no more genocide. Convinced, the president was about to green-light the operation.

But then his closest advisers convinced him to back down, claiming that with US troops already in Iraq and Afghanistan, an attack against another Muslim majority country would only increase hatred toward America and increase public sentiment against him. They persuaded him it was more important to solve his current problems. The attack against Sudan never took place. “Had the Israeli prime minister understood this dilemma,” the American official said, “he never would have expected Bush to order an air strike against the Syrian reactor.”

On June 19, 2007, a few months before the Israeli strike, Olmert arrived in Washington for a meeting with President Bush. While newspaper headlines claimed the leaders spoke about the Palestinian peace process, they spent the majority of their meeting discussing the nuclear reactor under construction in Syria.

“We plan to strike the reactor,” Olmert reportedly told the president. Bush tried to restrain him, suggesting alternative modes of action. From the American administration’s standpoint, a war between Israel and Syria would seriously damage the statebuilding process in Iraq and would even risk the stability of the Coalition in Afghanistan. But Israel’s prime minister politely explained that he was not there to ask the administration for permission; rather, he wanted to update him on Israel’s intentions.

“Israel was not looking for approval from the American government,” the top administration official explained. “Israel made it clear that there were no traffic lights and no requests for green lights or red lights.”

In his memoir Decision Points, published in November 2010, Bush himself supported this description. “Prime Minister Olmert hadn’t asked for a green light, and I hadn’t given one. He had done what he believed was necessary to protect Israel,” Bush wrote in his book.

The Israelis’ decision to inform the American administration of its plans derived from a few considerations. First, the Israeli government under Ehud Olmert enjoyed warm relations with the Bush administration.

In the meetings held in Israel prior to the attack, participants had raised the question of how it would affect Israel’s relationship with the United States. Some of the participants, like Ivry, remembered the aftermath of Operation Opera.

When Menachem Begin sent the IAF jets to strike Saddam Hussein’s nuclear reactor, Israel used American military equipment without prior coordination with the United States, and the US administration felt it had hurt the chances for peace in the Middle East. Two weeks after the 1981 attack the UN assembly approved a resolution denouncing Israel, with support from the United States, which usually prevented anti-Israel votes. The Reagan administration even decided to freeze deliveries of F- 16 fighter jets to Israel temporarily.

A decade later, however, when the American Army was fighting in Iraq, the administration recognized the importance of the Israeli operation.

The Olmert administration of 2007 showed it had learned its history lesson. Despite the Americans’ opposition, Olmert’s advisers still argued in favor of sharing the operation’s full itinerary with the Bush administration. This decision proved to be correct.

According to a senior official in the Bush administration, “From the beginning, both leaders said that Syria could not have a reactor. Bush agreed and was not disturbed with Israel’s actions, nor did it affect his relationship with Olmert.”

That same source also referred to the Israelis’ expectations that Bush would not leave office before stopping Iran’s nuclear program. “I think that an Israeli who knew of Bush’s decision not to bomb Sudan and Syria would have been hard-pressed to think that he was going to bomb Iran, which was a far more dangerous operation,” he said.

In Israel, which had proven twice that it is capable of destroying an enemy’s nuclear reactor, intelligence and operations officers continued to ponder the possibility of a third strike, this time against Iran.

They understood, though, that exerting political backbone, as Olmert had done, would not always be enough. After the successful bombing in Syria, one major question remained unresolved: how could Israel repeat its success in Iran?

This article is adapted from Israel vs. Iran: The Shadow War, published in May 2012 by Potomac Books. (© 1995-2011, The Jerusalem Post 06/08/12)