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Authors: Aki Peritz,Eric Rosenbach

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The Pentagon described the strike as a “pre-planned mission”—one of many on a list
30
—and secretary of defense Donald Rumsfeld seemed unprepared to discuss Atef’s death the following day.
31
US intelligence analysts probably knew that they were tracking down al-Qaeda and Taliban leaders, but not specifically focusing on Atef.
32
It was only when the US later intercepted communications from al-Qaeda members lamenting Atef’s death, that they deduced the identity of their victim.
33
According to one British official, an al-Qaeda operative broke security protocol after the attack and used a satellite phone to report on the casualties, a call that was intercepted by US and British signals intelligence.
34
Atef’s death was separately confirmed by a human source,
35
and the Taliban ambassador to Pakistan publicly announced it on November 18.
36
Even so, for months after the strike Atef remained on the FBI’s and the CIA’s list of most wanted al-Qaeda leaders—suggesting that they remained unsure about who had died.
37
Atef’s elimination may be linked to the defection of Mullah Mohammed Khaksar, once the Taliban’s deputy interior minister and head of the Taliban’s intelligence service, who was later gunned down in Kandahar in 2006.
38
Khaksar remained in Kabul as the rest of the Taliban fled—having negotiated a deal to switch sides before the Northern Alliance took the city—and had offered to help the US oust Taliban leadership even before 9/11.
39
He almost certainly had credible information on safe houses, communications networks, escape routes, and operating procedures, and had probably maintained a secret dialogue with the Northern Alliance and, to a lesser degree, the CIA.
40
In 2002 Khaksar complained that while he was ready to pass information on top al-Qaeda leaders and hideouts in Afghanistan to the US, nobody ever contacted him.
41
While the US had been lucky in fixing Atef, the means of finishing him may not have been ideal. A key element in the intelligence cycle is to debrief captured terrorist leaders. As one node reveals another, the whole network can be mapped out and taken down. Atef would have made an attractive capture for interrogation; as al-Qaeda’s senior operational planner, he would have known a wide section of the organization and had insight into all of its operations and capabilities. However, Atef was a hardened ideological fighter with few readily apparent weaknesses that might be exploited for advantage. He thoroughly believed in the cause, and possessed both a powerful physique and a formidable mind likely able to weave a web of deception even under duress.
THE WRONG GUY: ABU ZUBAYDAH (CAPTURED, MARCH 2002)
 
If Atef’s death appeared to demonstrate the power and reach of the US, the months to come seemed to highlight its limitations. Uncomfortable questions began to emerge: What would American forces do with individuals caught on the battlefield? Given the running conflict in Afghanistan, and the AUMF that authorized the almost unfettered ability for the US to prosecute the metastasizing war on terror, American forces, military or civilian, would inevitably capture more than a few suspects. Where would they go?
Two months after the 9/11 attacks saw allied Afghan and American forces shattering Taliban defenses in and around the capital, Kabul, and the final showdown with al-Qaeda was thought to be imminent. Bin Laden was still loitering in the city during the first week of the month, and even gave an interview to a Pakistani journalist Hamid Mir on November 8.
42
“Mark my words,” the al-Qaeda chief said, “[the Americans] can kill me anytime but they cannot capture me alive; they can claim victory only if they get me alive but if they will just capture my dead body, it will be a defeat.”
43
Four days later, Kabul fell to the Northern Alliance, but bin Laden and his al-Qaeda comrades managed to escape the tightening vise around the city and fled east toward Jalalabad. America’s endgame in Afghanistan was in sight—or so President Bush thought. The pivotal battle for Tora Bora, where bin Laden and his colleagues would slip away and eventually traverse the mountains into neighboring Pakistan—was still a month away.
Bush decided to answer one of the questions by casting battlefield-captured individuals into a legally ambiguous space. On November 13, the day after Kabul fell to the Northern Alliance, he signed a classified order—drafted by the vice president’s gruff, politically conservative adviser David Addington and White House counsel Alberto Gonzales a week before—authorizing military commissions to hold and interrogate the hundreds of men captured on the battlefield.
44
The order’s wording allowed great latitude and was remarkable for its underlying belief in maximalist executive power. The resulting military commission system could cast a wide net for individuals who were linked to al-Qaeda or conspired to participate in acts of terrorism. A panel would determine what sort of evidence was admissible, and decisions it made were final.
45
Detainees could be put to death if found guilty. Gonzales later wrote in a memo “this new paradigm renders obsolete [the Geneva Conventions’] strict limitations on questioning of enemy prisoners.”
46
These legal deliberations—the first of many—occurred behind closed doors while news of terror suspects being transferred soon spread. After 9/11, the White House was still stumbling to determine how to solve this new national security challenge but also saw an opportunity to concentrate diffused national security power in the hands of the president—to a degree not seen since the scandals of the Vietnam era.
More than one commentator found this disturbing, as the legal paradigm for prosecuting this new conflict continued to be hidden from view. “In the beginning,” recalled Mieke Eoyang, “it was all about theory. But when theory met reality, it was way outside what was the normal operating procedure for the US government.”
47
Perhaps the president relied on goodwill from a scared public amenable to his secrecy and overreach? “9/11 was not an excuse for what happened afterwards,” retorted Eoyang. “Remember, all this happened outside of public debate. There was no reason to create a legal framework in secret—the implementation can be secret, but the law itself should never be secret.”
48
And where would this exciting new legal paradigm unfold? The Pentagon selected America’s oldest overseas military base—the Guantanamo Bay naval station in Cuba—as the final stop for its captives in this shadowy conflict. Newly captured individuals, clad in orange jumpsuits, taken directly from the faraway battlefields of Afghanistan, began arriving at this tropical facility in early January 2002.
 
 
WILLIAM ARKIN
, a military consultant to Human Rights Watch and instructor at the US Air Force’s School of Advanced Airpower Studies, said that in the first two weeks of bombing, fewer than 10 percent of strikes directly targeted al-Qaeda; the campaign was set up as if the enemy were Iraq or Russia.
49
The US was trying to fight a conventional war against an unconventional foe. The Pentagon’s tactics had been strikingly effective in defeating the Taliban on the battlefield, but were much less effective in identifying senior leaders or eliminating al-Qaeda as a movement. “The inability to neutralize the core leadership of al-Qaeda and the Taliban in the first six months . . . is clearly the war on terrorism’s single biggest failure,” wrote Rohan Gunaratna, a consultant to the United Nations on terrorism.
50
CIA and other members of the IC still knew little about the identities and roles of key individuals in the organization—information that could only be gathered through human or technical means, not by killing prisoners outright. Detractors further complained that Special Forces frequently arrived too late in areas where al-Qaeda fighters had been hiding, and that the overreliance on local Afghan allies probably allowed bin Laden and other senior leaders to escape.
51
US military officials defended their strategy: the war had successfully ousted the Taliban, destroyed al-Qaeda’s safe haven, and deprived the terrorist network of the freedom to operate, train, and meet in Afghanistan.
52
This was true to an extent, but many intelligence analysts believed that the damage had been insufficient to cripple the terrorist network. “As people have been killed or captured, we have seen temporary blips in al-Qaeda operational activity, but not an overall decline,” said one American official.
53
After a leader was eliminated, another one stepped in to take his place and the organization remained strong.
Based on the organizational structure of al-Qaeda that was known at the time, several sources believed that Egyptian national Saif al-Adel would inherit Atef’s duties as operational commander.
54
Formerly a colonel in the Egyptian army, al-Adel was an experienced operative and had risen to become Atef’s right-hand man, as well as Zawahiri’s personal friend. Operational duties were often passed within narrow ethnic cliques; since al-Adel was Atef’s deputy and, like Atef and Zawahiri, an Egyptian, the fit made sense. But by early 2002, al-Adel had seemingly disappeared into Iran, and US officials were focusing on Palestinian Abu Zubaydah (Zayn al-Abidin Muhammad Husayn) as the new number 3.
55
Abu Zubaydah grew up in a middle-class Palestinian family in Saudi Arabia. As a teenager he relocated to the West Bank to join the Palestinian uprising against Israel.
56
There he became enamored with militant causes. Too young to be a veteran of the struggle against the Soviets, he traveled to Afghanistan in 1991 and apparently fought in the civil war that followed the Soviet retreat.
57
It was during this internecine conflict in Afghanistan that bin Laden came to know him and, over the next ten years, he acted as an administrator and facilitator for camps and guesthouses serving bin Laden’s network.
58
He also recruited Arab fighters in Pakistan and arranged their travel to various training camps and the frontlines of Bosnia and Chechnya.
59
By mid-2001, the CIA was tracking him as a senior al-Qaeda operative—citing his actions in pre-9/11 briefings to national security adviser Condoleezza Rice.
60
CIA agents would later describe him as intelligent, confident, self-assured, and disciplined; a “highly self-directed individual who prizes his independence.”
61
They maintained he was the coordinator of al-Qaeda’s unsuccessful millennium plot, a key planner in the 9/11 attacks, and, with Zawahiri, one of bin Laden’s top deputies.
62
They knew he acted as a freelance human resources officer, keeping a list of members and screening new recruits for operational training.
63
Some said he was
the
central link between the senior leadership and multiple operational cells overseas.
64
At the time of his capture, Abu Zubaydah was described as the highest-ranking al-Qaeda leader to fall into US hands, the “key terrorist recruiter and operational planner and member of bin Laden’s inner circle.”
65
US analysts may have believed this due to the frequency in which his name turned up in intelligence traffic—a side effect of his role as a travel and training coordinator—which left them with the impression that he was a major figure in the terrorist hierarchy.
66
President Bush named Abu Zubaydah as “one of the top three leaders” and “al-Qaeda’s chief of operations.”
Later evidence, however, seemed to indicate Abu Zubaydah was not nearly as important as they then assumed; he was more of a fixer for jihadist groups, not a formal member of al-Qaeda and certainly not the number 3 in the organization.
67
Some even said that he had severe mental problems, a war-wounded schizophrenic who was trusted with little more than making hotel and plane reservations.
68
Despite his dubious credentials as a terrorist mastermind, Abu Zubaydah was still a hard target. He had lived in Pakistan for years and had a myriad of contacts; he knew safe houses and travel routes. As al-Qaeda’s supposed travel and operations coordinator, he spoke several languages and had access to extensive resources, including false passports and aliases.
69
He was smart; he moved around frequently and covered his tracks, avoiding patterns.
70
The CIA discussed for months how to get rid of him.
71
But Abu Zubaydah made a mistake somewhere, perhaps not realizing the additional resources and momentum that the US had gained in Afghanistan. The CIA had begun to track and profile him as they catalogued his various aliases and associates, using information from captured documents, hard drives, maps, training manuals, intercepts, and former terrorist operatives. By understanding how he operated and with whom he associated, analysts could better fix his possible location. It would take time to decode, process, and piece together so much information but, by March 2002 the US had a much sharper picture of the terrorist network and had increased communications surveillance on many newly discovered al-Qaeda nodes overseas.
72
In late February 2002, CIA officers stationed in Islamabad received word from Agency headquarters that Abu Zubaydah was in Pakistan, probably in the dusty, overgrown city of Faisalabad.
73
According to one account, this initial break came from Pakistani ISI, who had noticed a caravan of very tall burqa-clad “women” (actually male operatives) traveling from the militant tribal area and had bribed the driver to learn their destination.
74
Using this information, the US mounted a major surveillance operation in the area, with sophisticated electronic equipment scanning the airwaves and teams of translators and analysts pouring over every fragment of intercepted communications. To parse the large amount of information being gathered, a Washington-based targeting analyst flew out to work with CIA field officers, and together they narrowed down the list of suspected hideouts to fourteen sites stretched across two cities.
75
Most were mud huts with thatched or corrugated tin roofs, but one—a modest middle-class residence identified as “Site X”—seemed to be especially important.
76
Realizing that it was understaffed for tackling fourteen safe houses simultaneously, the CIA assembled a larger team of FBI and Agency personnel and contacted
to plan a raid.

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