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Late last year, top Bush administration officials decided to take a step they had long resisted. They drafted a secret plan to authorize the Pentagon’s Special Operations forces to launch missions into the snowcapped 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 terror 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 U.S. counterterrorism agencies.

The new plan, outlined in a highly classified Pentagon order, was designed to eliminate some of those battles. And it was meant to pave an easier path into the tribal areas for U.S. 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 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 delay.

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

Just as it had on Sept. 10, 2001, Al Qaeda now has a band of terror camps from which to plan and train for attacks against Western targets. Officials say the new camps are smaller than the ones the group used before 2001. But despite dozens of U.S. missile strikes in Pakistan since 2002, one retired CIA officer estimated the makeshift training compounds have as many as 2,000 Arab and Pakistani militants, up from several hundred three years ago.

More than four dozen interviews in Washington and Pakistan suggest that the hunt for Al Qaeda in Pakistan, code-named Operation Cannonball by the CIA in 2006, was often undermined by bitter disagreements within the Bush administration and within the CIA, including about whether U.S. commandos should launch ground raids inside the tribal areas.

Inside the CIA, the fights included clashes between the agency’s outposts in Kabul, Afghanistan, and Islamabad. There also were battles between field officers and the counterterrorism center at CIA 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.”

Joint raids halted

An early arrangement that allowed U.S. 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 CIA officials in Pakistan questioned the accuracy of the intelligence and because aides to Defense Secretary Donald Rumsfeld believed the mission force had become too large.

Shortly after the Sept. 11 attacks, President Pervez Musharraf of Pakistan allowed U.S. forces to use Pakistani bases to support the U.S. invasion of Afghanistan, while Pakistani intelligence services worked closely with the CIA in tracking down Al Qaeda operatives. But from their vantage point in Afghanistan, the picture looked different to U.S. Special Operations forces, who saw signs that the militants whom the Americans had driven out of Afghanistan were regrouping on the Pakistani side.

Pakistanis were skeptical, however, including Gen. Ali Mohammad Jan Aurakzai, commander of forces in northwestern Pakistan, who was charged with searching for militants.

Former U.S. intelligence officials said Aurakzai’s sweeps were slow-moving and easily avoided. Robert Grenier, the CIA station chief in Islamabad from 1999 to 2002, said that Aurakzai was dismissive of the reports.

“Aurakzai and others didn’t want to believe it because it would have been an inconvenient fact,” Grenier recalled.

When U.S. military officials proposed in 2002 that Special Operations forces be allowed to establish bases in the tribal areas, Pakistan 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. U.S. forces felt the Pakistanis were limiting their movements. And while Pakistani officials publicly denied the presence of Americans, local tribesmen spotted the Americans and protested their presence.

Ground exit in 2003

Under pressure from Pakistan, the Bush administration decided in 2003 to end the U.S. military presence on the ground. To keep pressure on the Pakistanis about the tribal areas, officials decided to have Bush raise the issue in phone calls with Musharraf.

The conversations backfired. Two former U.S. officials say they were surprised and frustrated when instead of demanding action from Musharraf, Bush thanked him for his contributions to the war on terror.

Disagreements among officials at the Pentagon, Central Command and CIA led the U.S. to cancel an aggressive plan in 2005 to capture bin Laden’s top deputy, Ayman al-Zawahiri, in Pakistan.

After that, militants inside Pakistan 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 U.S. and NATO casualty rates by 45 percent.

Later that year the Pakistani government negotiated a cease-fire. But in the months following, cross-border incursions from the tribal areas into Afghanistan rose 300 percent.

Also that year, despite his initial misgivings and hesitation, Rumsfeld in November approved an operation to capture Sheik Saiid al-Masri, a top Al Qaeda operator in Pakistan. But that plan was put on hold days later after Rumsfeld was pushed out of office.

The decision last year to draw up the Pentagon order for a Special Operations campaign in the tribal areas was part of the effort to get Pakistan to step up its fight.

That the order remains unsigned reflects the bureaucratic fighting that persists, particularly from State Department officials opposed to any change that would allow military missions to be launched without the approval of the U.S. ambassador in Islamabad. With Al 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 CIA officials that the opportunity for decisive U.S. action against the militants may have been lost.

“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 RAND Corp.