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Authors: Aki Peritz,Eric Rosenbach

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It was only in late 2003 after al-Qaeda tried to kill Pakistani president Pervez Musharraf twice that he attracted the full attention of the Pakistani government. Al-Qaeda had been badly damaged by the new US-Pakistan relationship, and the organization apparently hoped that assassinating Musharraf would throw the country into political chaos and remove President Bush’s only real ally in Pakistan. Abu Faraj was ideally suited for such an operation, due to his connections with both Pakistani terrorist groups and members of the armed forces—some of whom were successfully recruited for the mission.
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Abu Faraj and his confederates planned two independent strikes: one designed to blow up a bridge while the president drove past it, and the other with two suicide bombers driving vehicles packed with explosives into Musharraf’s motorcade. Both missed assassinating the head of state, but the second effort killed nineteen people and exposed the weakness in Pakistan’s internal security net.
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Abu Faraj and his associates soon became some of the most hunted men in Pakistan.
With significant US help, Pakistani intelligence traced the vehicles and phones used in the attack and arrested one of Abu Faraj’s associates, Salahuddin Bhatti. According to Pakistani officials, it was Bhatti who first revealed Abu Faraj’s position in the al-Qaeda hierarchy.
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Computer expert Muhammad Naeem Noor Khan (a.k.a. Abu Talha) confirmed Abu Faraj’s role, while also revealing a hidden terror network in Britain.
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Later analysis of files and e-mails seized from Abu Talha’s computers uncovered detailed surveillance of financial institutions in New York City, Newark, and Washington, and demonstrated that the Pakistan-based wing of al-Qaeda—under Abu Faraj’s management—communicated with cells in the UK, and countries in both South and Southeast Asia.
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After winning a hard-fought reelection campaign in November 2004, the Bush administration was looking for another quick “victory” in the war on terror—and Pakistani officials, eager for further American financial and technological counterterrorism support, had incentive to paint Abu Faraj as one of al-Qaeda’s most important operatives. Pakistani officers finally apprehended Abu Faraj some thirty miles north of Peshawar on May 3, 2005. By the time he was captured, both US and Pakistani officials described him as al-Qaeda’s third most senior leader, subordinate only to bin Laden and Zawahiri, and director of all operations against the US and UK.
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Pakistani intelligence had missed catching Abu Faraj twice before. In the first instance, in April 2004, they had tracked down and arrested his driver. The interrogation led them to a man in the Punjab who had served as both a courier and host for the terrorist leader.
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The man told them that he had rented a house for Abu Faraj in nearby Abbottabad—the same city where American forces would discover bin Laden several years later. The Pakistanis raided the one house they had uncovered, but the wily terrorist operative moved between three houses to avoid discovery and was safely somewhere else.
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The second time, Pakistani intelligence was alerted to a meeting between two high-level al-Qaeda leaders at another house in Abbottabad, and set up an elaborate ambush to intercept them. But Abu Faraj cleverly sent a decoy ahead to test the waters and, when this individual approached the house, he triggered the ambush. In the resulting firefight, Pakistani officers killed the decoy and Abu Faraj, safe in his observation point, again escaped unharmed.
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By early 2005, the ISI managed to capture and recruit one of Abu Faraj’s Pakistani accomplices, giving them a key penetration into the organization. The asset gave the Pakistanis a critical advantage: they were able to set the stage for the encounter, rather than waiting for information on his location and hoping they could respond in time. Even so, Abu Faraj proved to be a cautious foe.
The recruited source arranged to meet Abu Faraj at 4:30 PM. Pakistani intelligence knew that he often traveled by motorbike with a driver, and so three officers on motorbikes planned to intercept him at the designated rendezvous point. Abu Faraj called his contact repeatedly to confirm the meeting but then declined to show up—perhaps wary of just such a setup. The next morning, however, Abu Faraj called to reschedule, giving Pakistani officers another slim shot. The source agreed to meet him at a famous shrine on the outskirts of the town of Mardan, some two hours west of Abbottabad, providing cover for both the elusive terrorist and the intelligence service. Preparing for the operation, several officers dressed as women in burqas and placed themselves among the crowd. At exactly 9:30 AM, Abu Faraj arrived wearing sunglasses and a cap and approached the ISI asset. As he passed by one of the disguised men, the officer jumped up and wrestled Abu Faraj to the ground.
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Some disagreement remains about what degree American cooperation contributed to Abu Faraj’s capture. In his memoirs, Musharraf paints the operation as a unilateral Pakistani success that came as a welcome surprise when he told Bush of the capture, and seems to make a point of downplaying the value of US technical assistance.
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But Pakistan may have been acting on American-provided information.
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A senior Pakistani intelligence official confirmed that the US had provided communications intercepts and information gathered in Afghanistan.
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Also, the US tracked Abu Faraj to Mardan through his satellite phone.
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There was reportedly disagreement between the CIA and ISI on how long to watch him once he had been fixed to some degree of precision. The Pakistanis were intent to apprehend the man who had tried to kill Musharraf, while the Americans hoped he might lead them to bin Laden—who might have been in Abbottabad by early 2005.
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With the capture of Abu Faraj, US intelligence officials believed they had a key source of new intelligence on al-Qaeda’s plans and operations. Unlike most other operatives, he was computer savvy and was believed to have detailed insight into how al-Qaeda units used coded and hidden communications to coordinate attacks.
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He was also a key contact for the top leadership; Abu Faraj eventually told interrogators that he was in contact with bin Laden through couriers, and that the last letter he had received was in December 2004.
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Pakistan took the first crack at his interrogation. According to Pakistani officials, they asked only two questions: “Where is bin Laden?” and “What are your plans?”
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It remains unclear whether the Pakistanis acquired any useful information during these initial rounds of questioning, despite the physical pressure they exerted. By tracing contacts on his mobile phone, however, Pakistani operatives uncovered and detained more than two dozen other al-Qaeda suspects in the subsequent weeks.
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Bowing to US pressure, Pakistani intelligence soon turned Abu Faraj over to American officials.
The capture of Abu Faraj was unquestionably a victory in the conflict with al-Qaeda. “If he’s a big fish, it’s because it’s a much smaller pond,” commented terrorism expert Bruce Hoffman at the time. Then again, “this movement has a knack for replacing serious operatives.”
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The war against al-Qaeda would continue.
 
 
THE REMOVAL
of the al-Qaeda number 3s represented significant signs of progress for the US—hard men were off the streets. But in its quest to crush al-Qaeda, America made some hard choices.
CHAPTER 4
 
THE FINISHING NEVER ENDS
 
How Far Will America Go?
 
 
 
 
Every thing secret degenerates, even the administration of justice; nothing is safe that does not show how it can bear discussion and publicity.
—LORD ACTON
 
 
 
 
R
awalpindi, March 2003.
The prisoner blinked unsteadily at his captors. Unshaven, obese, the man had been pulled out of bed by heavily armed intruders—but not before popping off a rifle round at his assailants, hitting one in the foot. As the prisoner was being dragged from the building, a photographer snapped a few photos. The prisoner was then stuffed into the black maw of a waiting vehicle.
So began Khalid Shaykh Mohammed’s long journey into the American justice system.
Mohammed—better known in the Western press by his initials, KSM—is the most important terrorist in US custody to date. The mastermind of the 9/11 attacks, KSM was also a significant player in half a dozen attempted attacks on US and allied sites and personnel dating back to the mid-1990s, including plots to assassinate President Clinton and Pope John Paul II. KSM was a one-man terrorist wrecking ball.
While a number of his colleagues, such as Mohammad Atef, met fiery ends courtesy of missiles launched from overhead aerial platforms, KSM was captured alive, allowing US authorities to use newly expanded national security tools such as rendition, enhanced interrogation techniques, and military commissions against him. US authorities have had some short- and medium-term successes likely attributable to KSM’s capture—terror plots halted in early stages, lives saved, and terror suspects removed from the streets. But his incarceration has also led to long-term political, legal, and ethical conundrums. How long can the US detain an individual without trial? Can the US legitimately use brutal methods, including torture, to elicit information from suspects, and then use that information—the fruit of the poison tree—against them in a court of law? Does KSM’s evolving legal status matter? And what does the treatment he receives at the hand of US authorities acting in an official capacity mean for the future of US national security actions against other suspected terrorists—or even US citizens?
The way KSM has been treated in US custody has become a Rorschach test for people discussing finishing techniques. Either he’s a terrorist of the first order, and nothing should be off-limits to extract intelligence or achieve justice (or revenge), or he’s the most famous victim of an overbearing, overreaching counterterrorism program that has shredded the US Constitution and has trampled on American values and decency. The example of KSM—and the treatment he received in US custody—serves as a cautionary tale about the ongoing issues that America’s new national security posture has brought. The fires and the fears of another attack following 9/11 have long since receded, but the US is now left with the consequences of its decisions from that time.
ORIGINS
 
Khalid Shaykh Mohammed was born in Kuwait on April 24, 1965, to Baluchs from Iran. His father, a conservative cleric, moved to the Persian Gulf in the early 1960s to take advantage of the riches found under the ground, but died when KSM was four years old.
1
KSM and his nephew, future 1993 World Trade Center attack mastermind Ramzi Yousef, were precocious expat kids and second-class citizens in the oil-rich Middle East. Drifting and searching for an identity, KSM reportedly joined the Muslim Brotherhood at age sixteen in what the CIA termed “an expression of his defiance against the secular world he saw around him.”
2
KSM enigmatically attended Chowan University, a small religious institution in North Carolina with a mission to provide “a caring environment characterized by Christian values and intellectual freedom in which students can gain the knowledge, skills, creativity, and ethical values they need to flourish in a rapidly changing, culturally diverse global society.” Chowan was not a good fit for the radical son of a Baluch cleric, and within a year KSM had transferred to another unlikely fit, the predominantly African American North Carolina Agricultural & Technical State University (NCA&T) across the state in Greensboro. KSM graduated from NCA&T in 1986 with a degree in mechanical engineering. During this time, he came to the conclusion, much as his Islamist predecessor Sayyid Qutb had a generation before, that the US was a racist, corrupt, debauched society. His impression of the country was not helped by a stint in a North Carolina jail cell over unspecified financial issues.
3
After graduation KSM left America to battle the Soviets in Afghanistan, drawn to the concept of violent jihad and the possibility of participating in it. There he linked up with the tireless purveyor of jihad, Abdullah Azzam, and the charismatic warlord Abdul Rasul Sayyaf, who had recently founded Ittihad-e-Islami and may have been the person who invited Osama bin Laden to Afghanistan.
4
Sayyaf, later a member of the Afghan parliament, was a major player in the Soviet-Afghan war, receiving funding from the Saudis and the US to fight the Red Army, and known by CIA case officers as one of the “seven dwarves.”
5
In late November 1989 a massive car bomb in Peshawar turned Azzam and his two sons into smoke, leaving KSM only one mentor. KSM would then exclusively work with Sayyaf, spending the next few years straddling the porous borderlands between Pakistan and Afghanistan.
Ramzi Yousef’s intense interest in striking the World Trade Center in New York City was pivotal in convincing KSM to attack the US. KSM backed Yousef financially, offering $1,000 to fund his WTC attack.
6
In an operation designed to blow up passenger aircraft in midair in the Philippines
,
KSM played a larger operational role alongside his nephew and made it onto the American intelligence radar screen. The US in the late 1990s considered a military option to nab KSM in Qatar where the minister of religious endowments, Shakyh Abdullah bin Khalid al-Thani, provided a measure of safe haven to Islamic militants. But the Qatari government dithered and delayed helping the US, and KSM was able to flee the country.
7

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