Amid Policy Disputes, Qaeda Grows in Pakistan

Monday, 30 June 2008 11:21 By Mark Mazzetti and David Rohde, The New York Times | name.

Amid Policy Disputes, Qaeda Grows in Pakistan
A soldier from Pakistan huddles in a bunker near the Afghan border. The fight against Taliban and al-Qaeda militants has become a source of major tension between Pakistan and the United States.
(Photo: Getty Images)

    Washington - Late last year, top Bush administration officials decided to take a step they had long resisted. They drafted a secret plan to make it easer for the Pentagon's Special Operations forces to launch missions into the snow-capped mountains of Pakistan to capture or kill top leaders of Al Qaeda.

    Intelligence reports for more than a year had been streaming in about Osama bin Laden's terrorism network rebuilding in the Pakistani tribal areas, a problem that had been exacerbated by years of missteps in Washington and the Pakistani capital, Islamabad, sharp policy disagreements, and turf battles between American counterterrorism agencies.

    The new plan, outlined in a highly classified Pentagon order, was intended to eliminate some of those battles. And it was meant to pave a smoother path into the tribal areas for American commandos, who for years have bristled at what they see as Washington's risk-averse attitude toward Special Operations missions inside Pakistan. They also argue that catching Mr. bin Laden will come only by capturing some of his senior lieutenants alive.

    But more than six months later, the Special Operations forces are still waiting for the green light. The plan has been held up in Washington by the very disagreements it was meant to eliminate. A senior Defense Department official said there was "mounting frustration" in the Pentagon at the continued delay.

    After the Sept. 11 attacks, President Bush committed the nation to a "war on terrorism" and made the destruction of Mr. bin Laden's network the top priority of his presidency. But it is increasingly clear that the Bush administration will leave office with Al Qaeda having successfully relocated its base from Afghanistan to Pakistan's tribal areas, where it has rebuilt much of its ability to attack from the region and broadcast its messages to militants across the world.

    A recent American airstrike killing Pakistani troops has only inflamed tensions along the mountain border and added to tensions between Washington and Pakistan's new government.

    The story of how Al Qaeda, whose name is Arabic for "the base," has gained a new haven is in part a story of American accommodation to President Pervez Musharraf of Pakistan, whose advisers played down the terrorist threat. It is also a story of how the White House shifted its sights, beginning in 2002, from counterterrorism efforts in Afghanistan and Pakistan to preparations for the war in Iraq.

    Just as it had on the day before 9/11, Al Qaeda now has a band of terrorist camps from which to plan and train for attacks against Western targets, including the United States. Officials say the new camps are smaller than the ones the group used prior to 2001. However, despite dozens of American missile strikes in Pakistan since 2002, one retired C.I.A. officer estimated that the makeshift training compounds now have as many as 2,000 local and foreign militants, up from several hundred three years ago.

    Publicly, senior American and Pakistani officials have said that the creation of a Qaeda haven in the tribal areas was in many ways inevitable - that the lawless badlands where ethnic Pashtun tribes have resisted government control for centuries were a natural place for a dispirited terrorism network to find refuge. The American and Pakistani officials also blame a disastrous cease-fire brokered between the Pakistani government and militants in 2006.

    But more than four dozen interviews in Washington and Pakistan tell another story. American intelligence officials say that the Qaeda hunt in Pakistan, code-named Operation Cannonball by the C.I.A. in 2006, was often undermined by bitter disagreements within the Bush administration and within the C.I.A., including about whether American commandos should launch ground raids inside the tribal areas.

    Inside the C.I.A., the fights included clashes between the agency's outposts in Kabul, Afghanistan, and Islamabad. There were also battles between field officers and the Counterterrorist Center at C.I.A. headquarters, whose preference for carrying out raids remotely, via Predator missile strikes, was derided by officers in the Islamabad station as the work of "boys with toys."

    An early arrangement that allowed American commandos to join Pakistani units on raids inside the tribal areas was halted in 2003 after protests in Pakistan. Another combat mission that came within hours of being launched in 2005 was scuttled because some C.I.A. officials in Pakistan questioned the accuracy of the intelligence, and because aides to Defense Secretary Donald H. Rumsfeld believed that the mission force had become too large.

    Current and former military and intelligence officials said that the war in Iraq consistently diverted resources and high-level attention from the tribal areas. When American military and intelligence officials requested additional Predator drones to survey the tribal areas, they were told no drones were available because they had been sent to Iraq.

    Some former officials say Mr. Bush should have done more to confront Mr. Musharraf, by aggressively demanding that he acknowledge the scale of the militant threat.

    Western military officials say Mr. Musharraf was instead often distracted by his own political problems, and effectively allowed militants to regroup by brokering peace agreements with them.

    Even critics of the White House agree that there was no foolproof solution to gaining control of the tribal areas. But by most accounts the administration failed to develop a comprehensive plan to address the militant problem there, and never resolved the disagreements between warring agencies that undermined efforts to fashion any coherent strategy.

    "We're just kind of drifting," said Richard L. Armitage, who as deputy secretary of state from 2001 to 2005 was the administration's point person for Pakistan.

    Fleeing US Air Power

    In March 2002, several hundred bedraggled foreign fighters - Uzbeks, Pakistanis and a handful of Arabs - fled the towering mountains of eastern Afghanistan and crossed into Pakistan's South Waziristan tribal area.

    Savaged by American air power in the battles of Tora Bora and the Shah-i-Kot valley, some were trying to make their way to the Arab states in the Persian Gulf. Some were simply looking for a haven.

    They soon arrived at Shakai, a remote region in South Waziristan of tree-covered mountains and valleys. Venturing into nearby farming villages, they asked local tribesmen if they could rent some of the area's walled family compounds, paying two to three times the impoverished area's normal rates as the militants began to lay new roots.

    "They slowly, steadily from the mountainside tried to establish communication," recalled Mahmood Shah, the chief civilian administrator of the tribal areas from 2001 to 2005.

    In many ways, the foreigners were returning to their home base. In the 1980s, Mr. bin Laden and hundreds of Arab and foreign fighters backed by the United States and Pakistan used the tribal areas as a staging area for cross-border attacks on Soviet forces in Afghanistan.

    The militants' flight did not go unnoticed by American intelligence agencies, which began to report beginning in the spring of 2002 that large numbers of foreigners appeared to be hiding in South Waziristan and neighboring North Waziristan.

    But Gen. Ali Mohammad Jan Aurakzai, the commander of Pakistani forces in northwestern Pakistan, was skeptical. In an interview this year, General Aurakzai recalled that he regarded the warnings as "guesswork," and said that his soldiers "found nothing," even when they pushed into dozens of square miles of territory that neither Pakistani nor British forces had ever entered.

    The general, a tall, commanding figure who was born in the tribal areas, was Mr. Musharraf's main adviser on the border areas, according to former Pakistani officials. For years, he would argue that American officials exaggerated the threat in the tribal areas and that the Pakistani Army should avoid causing a tribal rebellion at all costs.

    Former American intelligence officials said General Aurakzai's sweeps were slow-moving and easily avoided by militants. Robert L. Grenier, the C.I.A. station chief in Islamabad from 1999 to 2002, said that General Aurakzai was dismissive of the reports because he and other Pakistani officials feared the kind of tribal uprising that could have been touched off by more intrusive military operations. "Aurakzai and others didn't want to believe it because it would have been an inconvenient fact," Mr. Grenier recalled.

    Signs of Militants Regrouping

    Until recent elections pushed Mr. Musharraf off center stage in Pakistan, senior Bush administration officials consistently praised his cooperation in the Qaeda hunt.

    Beginning shortly after the Sept. 11 attacks, Mr. Musharraf had allowed American forces to use Pakistani bases to support the American invasion of Afghanistan, while Pakistani intelligence services worked closely with the C.I.A. in tracking down Qaeda operatives. But from their vantage point in Afghanistan, the picture looked different to American Special Operations forces who saw signs that the militants whom the Americans had driven out of Afghanistan were effectively regrouping on the Pakistani side of the border.

    When American military officials proposed in 2002 that Special Operations forces be allowed to establish bases in the tribal areas, Pakistan flatly refused. Instead, a small number of "black" Special Operations forces - Army Delta Force and Navy Seal units - were allowed to accompany Pakistani forces on raids in the tribal areas in 2002 and early 2003.

    That arrangement only angered both sides. American forces used to operating on their own felt that the Pakistanis were limiting their movements. And while Pakistani officials publicly denied the presence of Americans, local tribesmen spotted the Americans and protested.

    Under pressure from Pakistan, the Bush administration decided in 2003 to end the American military presence on the ground. In a recent interview, Mr. Armitage said he had supported the pullback in recognition of the political risks that Mr. Musharraf had already taken. "We were pushing them almost to the breaking point," Mr. Armitage said.

    The American invasion of Iraq in 2003 added another complicating factor, by cementing a view among Pakistanis that American forces in the tribal areas would be a prelude to an eventual American occupation.

    To have insisted that American forces be allowed to cross from Afghanistan into Pakistan, Mr. Armitage added, "might have been a bridge too far."

    Dealing With Musharraf

    Mr. Bush's re-election in 2004 brought with it another problem once the president overhauled his national security team. By early 2005, Secretary of State Colin L. Powell and Mr. Armitage had resigned, joining George J. Tenet, who had stepped down earlier as director of central intelligence. Their departures left the administration with no senior officials with close personal relationships with Mr. Musharraf.

    In order to keep pressure on the Pakistanis about the tribal areas, officials decided to have Mr. Bush raise the issue in personal phone calls with Mr. Musharraf.

    The conversations backfired. Two former United States government officials say they were surprised and frustrated when instead of demanding action from Mr. Musharraf, Mr. Bush repeatedly thanked him for his contributions to the war on terrorism. "He never pounded his fist on the table and said, 'Pervez you have to do this,'" said a former senior intelligence official who saw transcripts of the phone conversations. But another senior administration official defended the president, saying Mr. Bush had not gone easy on the Pakistani leader.

    "I would say the president pushes quite hard," said the official, who would speak about the confidential conversations only on condition of anonymity. At the same time, the official said Mr. Bush was keenly aware of the "unique burden" that rested on any head of state, and had the ability to determine "what the traffic will bear" when applying pressure to foreign leaders.

    Tensions Within the CIA

    As attacks into Afghanistan by militants based in the tribal areas continued, tensions escalated between the C.I.A. stations in Kabul and Islamabad, whose lines of responsibility for battling terrorism were blurred by the porous border that divides Afghanistan and Pakistan, and whose disagreements reflected animosities between the countries.

    Along with the Afghan government, the C.I.A. officers in Afghanistan expressed alarm at what they saw as a growing threat from the tribal areas. But the C.I.A. officers in Pakistan played down the problem, to the extent that some colleagues in Kabul said their colleagues in Islamabad were "drinking the Kool-Aid," as one former officer put it, by accepting Pakistani assurances that no one could control the tribal areas.

    On several occasions, senior C.I.A. officials at agency headquarters had to intervene to dampen tensions between the dueling C.I.A. outposts. Other intragovernmental battles raged at higher altitudes, most notably over the plan in early 2005 for a Special Operations mission intended to capture Ayman al-Zawahri, Mr. bin Laden's top deputy, in what would have been the most aggressive use of American ground troops inside Pakistan. The New York Times disclosed the aborted operation in a 2007 article, but interviews since then have produced new details about the episode.

    As described by current and former government officials, Mr. Zawahri was believed by intelligence officials to be attending a meeting at a compound in Bajaur, a tribal area, and the plan to send commandos to capture him had the support of Porter J. Goss, the C.I.A. director, and the Special Operations commander, Lt. Gen. Stanley A. McChrystal.

    But even as members of the Navy Seals and Army Rangers in parachute gear were boarding C-130 cargo planes in Afghanistan, there were frenzied exchanges between officials at the Pentagon, Central Command and the C.I.A. about whether the mission was too risky. Some complained that the American commando force was too large, numbering more than 100, while others argued that the intelligence was from a single source and unreliable.

    Mr. Goss urged the military to carry out the mission, and some C.I.A. officials in Washington even tried to give orders to execute the raid without informing Ryan C. Crocker, then the American ambassador in Islamabad. But other C.I.A. officials were opposed to the raid, including a former officer who said in an interview that he had "told the military guys that this thing was going to be the biggest folly since the Bay of Pigs."

    In the end, the mission was aborted after Mr. Rumsfeld refused to give his approval for it. The decision remains controversial, with some former officials seeing the episode as a squandered opportunity to capture a figure who might have led the United States to Mr. bin Laden, while others dismiss its significance, saying that there had been previous false alarms and that there remained no solid evidence that Mr. Zawahri was present.

    Bin Laden Hunt at Dead End

    By late 2005, many inside the C.I.A. headquarters in Virginia had reached the conclusion that their hunt for Mr. bin Laden had made little progress since Tora Bora.

    Jose A. Rodriguez Jr., who at the time ran the C.I.A.'s clandestine operations branch, decided in late 2005 to make a series of swift changes to the agency's counterterrorism operations.

    He replaced Mr. Grenier, the former Islamabad station chief who in late 2004 took over as head of the agency's Counterterrorist Center. The two men had barely spoken for months, and some inside the agency believed this personality clash was beginning to affect C.I.A. operations.

    Mr. Grenier had worked to expand the agency's counterterrorism focus, reinforcing operations in places like the Horn of Africa, Southeast Asia and North Africa. He also reorganized and renamed Alec Station, the secret C.I.A. unit formed in the 1990s to hunt Al Qaeda.

    Mr. Grenier believed that the Counterterrorist Center and Alec Station had both grown very rapidly since 2001 and needed to be restructured to eliminate overlap.

    But Mr. Rodriguez believed that the Qaeda hunt had lost its focus on Mr. bin Laden and the militant threat in Pakistan.

    So he appointed a new head of the Counterterrorist Center, who has not been publicly identified, and sent dozens more C.I.A. operatives to Pakistan. The new push was called Operation Cannonball, and Mr. Rodriguez demanded urgency, but the response had a makeshift air.

    There was nowhere to house an expanding headquarters staff, so giant Quonset huts were erected outside the cafeteria on the C.I.A.'s leafy Virginia campus to house a new team assigned to the bin Laden mission. In Pakistan, the new operation was staffed not only with C.I.A. operatives drawn from around the world, but also with recent graduates of "the Farm," the agency's training center at Camp Peary in Virginia.

    "We had to put people out in the field who had less than ideal levels of experience," one former senior C.I.A. official said. "But there wasn't much to choose from."

    One reason for this, according to two former intelligence officials directly involved in the Qaeda hunt, was that by 2006 the Iraq war had drained away most of the C.I.A. officers with field experience in the Islamic world. "You had a very finite number" of experienced officers, said one former senior intelligence official. "Those people all went to Iraq. We were all hurting because of Iraq."

    Surge in Suicide Bombings

    The increase had little impact in Pakistan, where militants only continued to gain strength. In the spring of 2006, Taliban leaders based in Pakistan launched an offensive in southern Afghanistan, increasing suicide bombings by sixfold and American and NATO casualty rates by 45 percent. At the same time, they assassinated tribal elders in Pakistan who were cooperating with the government.

    Once again, Pakistani Army units launched a military campaign in the tribal areas. Once again, they suffered heavy casualties.

    And once again, Mr. Musharraf turned to General Aurakzai to deal with the problem. Having retired from the Pakistani Army, General Aurakzai had become the governor of North-West Frontier Province, and he immediately began negotiating with the militants. On Sept. 5, 2006, General Aurakzai signed a truce with militants in North Waziristan, one in which the militants agreed to surrender to local tribes and carry out no further attacks in Afghanistan.

    To help sell Washington on the deal, Mr. Musharraf brought General Aurakzai to the Oval Office several weeks later.

    In a presentation to Mr. Bush, General Aurakzai advocated a strategy that would rely even more heavily on cease-fires, and said striking deals with the Taliban inside Afghanistan could allow American forces to withdraw from Afghanistan within seven years.

    But the cease-fire in Waziristan had disastrous consequences. In the months after the agreement was signed, cross-border incursions from the tribal areas into Afghanistan rose by 300 percent. Some American officials began to refer to General Aurakzai as a "snake oil salesman."

    A Rising Terror Threat

    By the fall of 2006, the top American commander in Afghanistan had had enough.

    Intelligence reports were painting an increasingly dark picture of the terrorism threat in the tribal areas. But with senior Bush administration officials consumed for much of that year with the spiraling violence in Iraq, the Qaeda threat in Pakistan was not at the top of the White House agenda.

    Mr. Bush had declared in a White House news conference that fall that Al Qaeda was "on the run."

    To get Washington's attention, the commander, Lt. Gen. Karl W. Eikenberry, ordered military officers, Special Operations forces and C.I.A. operatives to assemble a dossier showing Pakistan's role in allowing militants to establish a haven.

    Behind the general's order was a broader feeling of outrage within the military - at a terrorist war that had been outsourced to an unreliable ally, and at the grim fact that America's most deadly enemy had become stronger.

    For months, military officers inside a walled-off compound at Bagram Air Base in Afghanistan, where a branch of the military's classified Joint Special Operations Command is based, had grown increasingly frustrated at what they saw as missed opportunities in the tribal areas.

    American commanders had been pressing for much of 2006 to get approval from Mr. Rumsfeld for an operation to capture Sheik Saiid al-Masri, a top Qaeda operator and paymaster whom American intelligence had been tracking in the Pakistani mountains.

    Mr. Rumsfeld and his staff were reluctant to approve the mission, worried about possible American military casualties and a popular backlash in Pakistan.

    Finally, in November 2006, Mr. Rumsfeld approved a plan for Navy Seal and Army Delta Force commandos to move into Pakistan and capture Mr. Masri. But the operation was put on hold days later, after Mr. Rumsfeld was pushed out of the Pentagon, a casualty of the Democratic sweep of the 2006 election.

    When General Eikenberry presented his dossier to several members of Mr. Bush's cabinet, some inside the State Department and the C.I.A. dismissed the briefing as exaggerated and simplistic. But the White House took note of his warnings, and decided to send Vice President Dick Cheney to Islamabad in March 2007, along with Stephen R. Kappes, the deputy C.I.A. director, to register American concern.

    That visit was the beginning of a more aggressive effort by the administration to pressure Pakistan's government into stepping up its fight. The decision last year to draw up the Pentagon order authorizing for a Special Operations campaign in the tribal areas was part of that effort.

    But the fact that the order remains unsigned reflects the infighting that persists. Administration lawyers and State Department officials are concerned about any new authorities that would allow military missions to be launched without the approval of the American ambassador in Islamabad. With Qaeda operatives now described in intelligence reports as deeply entrenched in the tribal areas and immersed in the civilian population, there is also a view among some military and C.I.A. officials that the opportunity for decisive American action against the militants may have been lost.

    Pakistani military officials, meanwhile, express growing frustration with the American pressure, and point out that Pakistan has lost more than 1,000 members of its security forces in the tribal areas since 2001, nearly double the number of Americans killed in Afghanistan.

    Some architects of America's efforts in Pakistan defend the Bush administration's record in the tribal areas, and vigorously deny that Washington took its eye off the terrorist threat as it focused on Iraq policy. Some also question whether Mr. bin Laden and Mr. Zawahri, Al Qaeda's top two leaders, are really still able to orchestrate large-scale attacks.

    "I do wonder if it's in fact the case that Al Qaeda has really reconstituted itself to a pre-9/11 capability, and in fact I would say I seriously doubt that," said Mr. Crocker, the American ambassador to Pakistan between 2004 and 2006 and currently the ambassador to Iraq.

    "Their top-level leadership is still out there, but they're not communicating and they're not moving around. I think they're symbolic more than operationally effective," Mr. Crocker said.

    But while Mr. Bush vowed early on that Mr. bin Laden would be captured "dead or alive," the moment in late 2001 when Mr. bin Laden and his followers escaped at Tora Bora was almost certainly the last time the Qaeda leader was in American sights, current and former intelligence officials say. Leading terrorism experts have warned that it is only a matter of time before a major terrorist attack planned in the mountains of Pakistan is carried out on American soil.

    "The United States faces a threat from Al Qaeda today that is comparable to what it faced on Sept. 11, 2001," said Seth Jones, a Pentagon consultant and a terrorism expert at the RAND Corporation.

    "The base of operations has moved only a short distance, roughly the difference from New York to Philadelphia."

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    Mark Mazzetti reported from Washington, and David Rohde from Washington and Islamabad, Peshawar and Rawalpindi, Pakistan. David E. Sanger contributed reporting from Washington.

Last modified on Monday, 30 June 2008 12:04