Things looked pretty ominous for al-Qaeda in 2003 and 2004. In the State of the Union speeches from those years and the infamous “Mission Accomplished” speech from May 2003, George W. Bush touted the military advances made on the organization that financed, planned and executed the attacks of September 11, 2001:

“All told, more than 3,000 suspected terrorists have been arrested in many countries. Many others have met a different fate. Let’s put it this way—they are no longer a problem to the United States and our friends and allies.”

“We have the terrorists on the run. We’re keeping them on the run. One by one, the terrorists are learning the meaning of American justice.”

“We’re tracking al Qaeda around the world, and nearly two-thirds of their known leaders have now been captured or killed.”

“[A]s of tonight, nearly one-half of al Qaeda’s senior operatives have been captured or killed.”
“As we fight this war, we will remember where it began—here, in our own country.”

It seems, however, that the Bush administration doesn’t remember how it began and who started it.

From a recently published National Intelligence Estimate, we find that al-Qaeda (spelled Al-Qa’ida in the NIE) is as strong as it was before 9/11 and is safely ensconced in northwest Pakistan. Some quotes:
“Al-Qa’ida is and will remain the most serious terrorist threat to the [U.S.] Homeland, as its central leadership continues to plan high-impact plots, while pushing others in extremist Sunni communities to mimic its efforts and to supplement its capabilities. We assess the group has protected or regenerated key elements of its Homeland attack capability, including: a safehaven in the Pakistan Federally Administered Tribal Areas (FATA), operational lieutenants, and its top leadership. Although we have discovered only a handful of individuals in the United States with ties to al-Qa’ida senior leadership since 9/11, we judge that al-Qa’ida will intensify its efforts to put operatives here.”

“We assess that al-Qa’ida will continue to enhance its capabilities to attack the Homeland through greater cooperation with regional terrorist groups. Of note, we assess that al-Qa’ida will probably seek to leverage the contacts and capabilities of al-Qa’ida in Iraq (AQI), its most visible and capable affiliate and the only one known to have expressed a desire to attack the Homeland. In addition, we assess that its association with AQI helps al-Qa’ida to energize the broader Sunni extremist community, raise resources, and to recruit and indoctrinate operatives, including for Homeland attacks.”

This report highlights three major mistakes on the part of the Bush administration.
1) Taking the eye off the ball of al-Qaeda and becoming distracted by Iraq. There are approximately 19,000 troops (coalition, not just U.S.) in Afghanistan. There are about 160,000 U.S. troops in Iraq. As the focus has strayed from al-Qaeda to Iraq, al-Qaeda has slowly and effectively reconstituted itself in Pakistan (visualize the creepy mercury-like terminator in T-2). Essentially, the bad guys of 9/11 have had time and quarter to regroup while the Bush administration has chased a different rabbit.
2) Failing to execute operations in Iraq well enough to stop AQI’s infiltration, terrorism, and recruitment efforts in Iraq. Al-Qaeda didn’t exist in Iraq before the U.S. invaded. But since then, Iraq has become a favorite location for al-Qaeda to recruit and train new members. It has also used the war in Iraq as a wedge to drive susceptible Sunnis to extremism. Essentially, the administration’s bungled attempt at war has exacerbated the situation by giving al-Qaeda a foothold and recruiting ground in yet another country.
3) Failing to hold Pakistan sufficiently responsible and accountable for activities within its borders. According to a July 8, 2007 New York Times story, “A secret military operation in early 2005 to capture senior members of al Qaeda in Pakistan’s tribal areas was aborted at the last minute after top Bush administration officials decided it was too risky and could jeopardize relations with Pakistan, according to intelligence and military officials.” Donald Rumsfeld, then the Secretary of War, was “concerned that it could cause a rift with Pakistan.” Pakistan’s tribal areas have “become virtual havens for the terrorist network.” This is all because we need Pakistan’s help in the war against terror? Well, obviously we aren’t getting it. Pakistan has no incentive to find Osama Bin Laden in Pakistan because 1) they have already said he’s not there, and 2) it might require the presence of U.S. and coalition forces. All of Bush’s talk of letting the generals run the war instead of the politicians sounds really hollow in light of this information.

The first two mistakes are over and done—the bell can’t be unrung. This third point, however, is an ongoing problem. If the administration continues to focus on Iraq and treat Pervez Musharaf with kid-gloves, we’ll never see the killers of 9/11 brought to justice, despite all the tough talk over the years.