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In December 2001, after the Singaporean JI members were arrested, Hambali told Jabarah to flee to Southeast Asia. He went instead to the United Arab Emirates. KSM told him to travel to Oman to set up a safe house for al-Qaeda members fleeing Afghanistan and heading to Yemen. In Oman Jabarah was arrested.

The ISD commander overseeing the operation against the group in Singapore, Brian, had his team of investigators watching almost a hundred people, and he would have liked to watch the plot mature further, as there were still many unanswered questions: Who else was involved in the plot? How extensive was this terrorist network in Singapore and the region? How were these groups linked to al-Qaeda? And what other acts of violence were they planning?

Brian, a seasoned investigator and commander who had honed his interrogation skills on espionage cases and had a nonconfrontational style that encouraged suspects to talk, had his hand forced after the press reported that Aslam had been arrested by the Northern Alliance in Afghanistan. His teams moved in, and in a series of raids (the last of which was December 24, 2001), a total of twenty-three men were arrested. Those who were not positively identified as group members were allowed to flee with their families to Malaysia, as the ISD was confident that they could track them if they returned.

At Singapore’s Whitley Road Detention Centre, the head of ISD, Andrew, reviewed the case in Brian’s office. Standing before a flip chart, Andrew began reworking the organization’s structure in his cursive script as investigators pointed out subordinate cells they had uncovered, spelled out names, and debated the role of peripheral characters.

When they had first mentioned the name Jemaah Islamiah, liaison security services didn’t have any information, and one had even laughed dismissively: “It means ‘Islamic community.’ Why should it concern us?” But what the ISD had discovered was a pan–Southeast Asian terrorist network with multiple cells in Singapore, Malaysia, Indonesia, and the Philippines and with direct links to al-Qaeda in Afghanistan.

Just as 1979 had been a pivotal year for al-Qaeda, it was also a very important year for Islamist terrorist groups in Southeast Asia. Members of many organizations traveled to Afghanistan to help fight the Soviets and also to experience the “thrill” of jihad and victory over a superpower.

Not without reason did a January 2003 Singapore government white paper on JI label the Soviet jihad as “perhaps the most significant factor in the radicalization of the militant Islamic groups in the region.” Abdullah Sungkar, who went on to found Jemaah Islamiah with the cleric Abu Bakar Bashir and other senior Darul Islam members, had traveled to Afghanistan in the 1980s to arrange for his members to participate in the jihad. They maintained a connection with operatives who went on to form al-Qaeda. By the mid-1990s select JI members were being sent to train in al-Qaeda camps in Afghanistan, learning “sophisticated terrorist tradecraft and expertise,” as the white paper reports, and “they transferred the skills to other members of their organizations.” They forged links with other terrorist groups based in Southeast Asia whose members had fought in Afghanistan, including the Moro Islamic Liberation Front.

The Afghanistan connection gave al-Qaeda members easy access to Southeast Asia. A number of JI members I later spoke with told me that they had met KSM and other al-Qaeda members when they went through the region. Khallad and 9/11 hijackers Khalid al-Mihdhar and Nawaf al-Hazmi passed through Southeast Asia between December 1999 and January 2000, and Hambali helped with their lodging and travel. Hambali was central to cementing the relationship between al-Qaeda and JI. A disciple of Sungkar, he had been sent by him to train in Afghanistan in 1986, where he also fought the Soviets. He remained in the country for eighteen months, building a relationship with KSM in the process.

As with other regional terrorist groups it tried to co-opt, al-Qaeda funded JI, thereby tying the two groups to each other. While Hambali embraced al-Qaeda and swore allegiance to bin Laden, other JI members resisted the connection, preferring to focus on their near enemy rather than al-Qaeda’s far enemy, the United States.

Other JI commanders I later spoke to, including Nasir Abbas, told me that they had opposed Hambali and had refused to endorse his operations. He had control over Singapore and Malaysia, which is where al-Qaeda’s initial focus in the region was because that was where its members were. At times he managed to bypass local commanders and run operations in their fiefdoms, including in Indonesia itself. Hambali’s efforts were helped after Sungkar died, in 1999, and Abu Bakar Bashir took over. Bashir supported Hambali’s relationship with al-Qaeda and gave Hambali freedom to do almost whatever he liked.

December 13, 2001. Hambali was furious when he learned of the arrests in Singapore. This was yet another failure for him: he had orchestrated a series of bombings of Christian churches across the Indonesian archipelago on Christmas Eve 2000, but several of the bombs had been badly placed and had failed to kill anyone. Still, 19 people died that night, and 120 were injured, in what came to be known as the Christmas Eve bombings. With the Singapore plan in ruins and key operatives in custody, Hambali decided to improvise and met several of the Singapore JI fugitives in Johor on December 13. He ordered them to bomb targets in Singapore to retaliate against the arrests. He found an eager terrorist conspirator in Mas Selamat Kastari, who had taken over as operational commander of the Singapore JI network from Ibrahim Maidin in 1999, and gave him approval to hijack a Singapore-bound airplane and crash it into Changi Airport, Singapore’s international airport, in what an accomplice would later describe, referring to the World Trade Center, as “a WTC on Changi.”

The group had previously identified the airport as a potential target and had taken reconnaissance photos, so with the legwork already done, Mas Selamat handpicked four of his most trusted cell members and accompanied them to Thailand. Hiding out in the seaside resort of Pattaya, they bought five business-class tickets on Aeroflot to Singapore and planned the details of their attack. (The choice of a Russian airline was deliberate; Kastari wanted to avenge the killing of Chechen Muslims by Russian soldiers.)

ISD broke up the plot. On December 29 it alerted all its security partners, and Mas Selamat’s photo appeared on the front pages of Thai newspapers. Their cover blown, Mas Selamat and his cell were forced to flee Thailand. ISD tracked Mas Selamat down in Riau a year later and informed the Indonesian police, who arrested and jailed him for immigration violations. He was eventually deported to Singapore in 2006, as were two of his accomplices.

In 2001, the Indonesian government of Megawati Soekarnoputri was ambivalent about the threat posed by Jemaah Islamiah. The government’s complacency was reinforced when Singaporean authorities named the Indonesian cleric Abu Bakar Bashir as the spiritual leader of JI. But while Bashir appeared to be harmless and well respected, in reality he was firmly committed to violence and had let Hambali effectively run the group. Megawati’s own vice president led the chorus of skeptics who muttered darkly about Western conspiracies, insisting that Jemaah Islamiah simply meant Islamic community. All that changed on October 12, 2002, when two massive bombs ripped through the heart of Bali. This was the second anniversary of the USS Cole attack, a thought that immediately went through my mind when I heard the news.

Hambali’s first successful operation in Indonesia was the bombing of the Filipino ambassador in Jakarta in August 2000. While the ambassador’s Mercedes-Benz withstood the blast of the parcel bomb left outside his front gate (it was detonated as his car drove in), he was badly injured, and an Indonesian guard at the gate and a street vendor were killed.