"Early successes in these campaigns - disrupting command and control centers, and taking away safe havens - have only yielded a franchised and networked enemy that is more diffuse, an ideological movement that is no longer tethered to any strict hierarchy," the Pentagon chief said in the most downbeat assessment he has given on the Bush administration's progress in the war on terror.
"It has become an independent force of its own, capable of animating a corps of devoted followers without direct contact and capable of inspiring violence without direct orders," Gates told a gathering of special operations forces, the military commandos who lead the U.S.-declared war on terrorism.
Gates also said the threat of those groups using chemical, biological, radiological, nuclear or cyber weapons is growing.
But he argued that Iraq and Afghanistan offered the United States its best opportunity to defeat al Qaeda and affiliated groups. He warned against pulling out of Iraq -- a move favored by leading Democrats including presidential candidates Barack Obama and Hillary Clinton -- and said winning both wars would "strike a decisive blow against the ideological underpinnings of extremist movements."
Gates also said military operations in Iraq and Afghanistan offered a model of the skills that he said the United States would need in counterterrorism operations elsewhere.
'THE LONG WAR'
"Other fronts in the long war will not look the same but they will use the same basic tactics," Gates said in his prepared remarks.
"They will, in all likelihood be on a much, much smaller scale - with special operations forces as the main component - focused on training elite indigenous forces, gathering intelligence, targeting ringleaders and support networks, and working with other elements of our government to help promote political, civil, and economic development."
He called that special operations-focused strategy for counterterrorism "persuasion" and compared it to deterrence, a Cold War-era strategy to deter a strike by the Soviet Union and other potential adversaries by posing a credible threat of immense retaliation.
The goal of persuasion, Gates said, is to encourage people to support their governments rather than extremist groups and to convince those who finance, recruit and provide safe havens to extremist groups that their efforts are futile.
The U.S. military's secretive Special Operations Command and its 54,000 troops are responsible for the U.S. war on terrorism. While those special forces operate in more than 60 countries, the vast majority - 80 percent - are in Iraq and Afghanistan.
Special Operations Command, based in Florida, will expand over the next three years, partly to meet the strain from Iraq and Afghanistan but also on expectations that counterterrorism operations will be conducted for decades to come.
"They will be in Iraq and Afghanistan for an extended period of time - as a force to hunt and kill terrorists and also as a force to help train Iraqis and Afghans," Gates said.