By SCOTT SHANE, MARK MAZZETTI and ROBERT F. WORTH

Published: August 14, 2010

WASHINGTON — At first, the news from Yemen on May 25 sounded like a modest victory in the campaign against terrorists: an airstrike had hit a group suspected of being operatives for Al Qaeda in the remote desert of Marib Province, birthplace of the legendary queen of Sheba. But the strike, it turned out, had also killed the province’s deputy governor, a respected local leader who Yemeni officials said had been trying to talk Qaeda members into giving up their fight. Yemen’s president, Ali Abdullah Saleh, accepted responsibility for the death and paid blood money to the offended tribes. The strike, though, was not the work of Mr. Saleh’s decrepit Soviet-era air force. It was a secret mission by the United States military, according to American officials, at least the fourth such assault on Al Qaeda in the arid mountains and deserts of Yemen since December. The attack offered a glimpse of the Obama administration’s shadow war against Al Qaeda and its allies. In roughly a dozen countries — from the deserts of North Africa, to the mountains of Pakistan, to former Soviet republics crippled by ethnic and religious strife — the United States has significantly increased military and intelligence operations, pursuing the enemy using robotic drones and commando teams, paying contractors to spy and training local operatives to chase terrorists. The White House has intensified the Central Intelligence Agency’s drone missile campaign in Pakistan, approved raids against Qaeda operatives in Somalia and launched clandestine operations from Kenya. The administration has worked with European allies to dismantle terrorist groups in North Africa, efforts that include a recent French strike in Algeria. And the Pentagon tapped a network of private contractors to gather intelligence about things like militant hide-outs in Pakistan and the location of an American soldier currently in Taliban hands. While the stealth war began in the Bush administration, it has expanded under President Obama, who rose to prominence in part for his early opposition to the invasion of Iraq. Virtually none of the newly aggressive steps undertaken by the United States government have been publicly acknowledged. In contrast with the troop buildup in Afghanistan, which came after months of robust debate, for example, the American military campaign in Yemen began without notice in December and has never been officially confirmed. Obama administration officials point to the benefits of bringing the fight against Al Qaeda and other militants into the shadows. Afghanistan and Iraq, they said, have sobered American politicians and voters about the staggering costs of big wars that topple governments, require years of occupation and can be a catalyst for further radicalization throughout the Muslim world. Instead of “the hammer,” in the words of John O. Brennan, President Obama’s top counterterrorism adviser, America will rely on the “scalpel.” In a speech in May, Mr. Brennan, an architect of the White House strategy, used this analogy while pledging a “multigenerational” campaign against Al Qaeda and its extremist affiliates. Yet such wars come with many risks: the potential for botched operations that fuel anti-American rage; a blurring of the lines between soldiers and spies that could put troops at risk of being denied Geneva Convention protections; a weakening of the Congressional oversight system put in place to prevent abuses by America’s secret operatives; and a reliance on authoritarian foreign leaders and surrogates with sometimes murky loyalties. The May strike in Yemen, for example, provoked a revenge attack on an oil pipeline by local tribesmen and produced a propaganda bonanza for Al Qaeda in the Arabian Peninsula. It also left President Saleh privately furious about the death of the provincial official, Jabir al-Shabwani, and scrambling to prevent an anti-American backlash, according to Yemeni officials. The administration’s demands have accelerated a transformation of the C.I.A. into a paramilitary organization as much as a spying agency, which some critics worry could lower the threshold for future quasi-military operations. In Pakistan’s mountains, the agency had broadened its drone campaign beyond selective strikes against Qaeda leaders and now regularly obliterates suspected enemy compounds and logistics convoys, just as the military would grind down an enemy force. For its part, the Pentagon is becoming more like the C.I.A. Across the Middle East and elsewhere, Special Operations troops under secret “Execute Orders” have conducted spying missions that were once the preserve of civilian intelligence agencies. With code names like Eager Pawn and Indigo Spade, such programs typically operate with even less transparency and Congressional oversight than traditional covert actions by the C.I.A. And, as American counterterrorism operations spread beyond war zones into territory hostile to the military, private contractors have taken on a prominent role, raising concerns that the United States has outsourced some of its most important missions to a sometimes unaccountable private army. A Proving Ground Yemen is a testing ground for the “scalpel” approach Mr. Brennan endorses. Administration officials warn of the growing strength of Al Qaeda’s affiliate there, citing as evidence its attempt on Dec. 25 to blow up a trans-Atlantic jetliner using a young Nigerian operative. Some American officials believe that militants in Yemen could now pose an even greater threat than Al Qaeda’s leadership in Pakistan.