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 and Mauritanian strike near the border between Mauritania and Mali. 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.

The officials said that they have benefited from the Yemeni government’s new resolve to fight Al Qaeda and that the American strikes — carried out with cruise missiles and Harrier fighter jets — had been approved by Yemen’s leaders. The strikes, administration officials say, have killed dozens of militants suspected of plotting future attacks. The Pentagon and the C.I.A. have quietly bulked up the number of their operatives at the embassy in Sana, the Yemeni capital, over the past year.

“Where we want to get is to much more small scale, preferably locally driven operations,” said Representative Adam Smith, Democrat of Washington, who serves on the Intelligence and Armed Services Committees.

“For the first time in our history, an entity has declared a covert war against us,” Mr. Smith said, referring to Al Qaeda. “And we are using similar elements of American power to respond to that covert war.”

Some security experts draw parallels to the cold war, when the United States drew heavily on covert operations as it fought a series of proxy battles with the Soviet Union.

And some of the central players of those days have returned to take on supporting roles in the shadow war. Michael G. Vickers, who helped run the C.I.A.’s campaign to funnel guns and money to the Afghanistan mujahedeen in the 1980s and was featured in the book and movie “Charlie Wilson’s War,” is now the top Pentagon official overseeing Special Operations troops around the globe. Duane R. Clarridge, a profane former C.I.A. officer who ran operations in Central America and was indicted in the Iran-contra scandal, turned up this year helping run a Pentagon-financed private spying operation in Pakistan.

In pursuing this strategy, the White House is benefiting from a unique political landscape. Republican lawmakers have been unwilling to take Mr. Obama to task for aggressively hunting terrorists, and many Democrats seem eager to embrace any move away from the long, costly wars begun by the Bush administration.

Still, it has astonished some old hands of the military and intelligence establishment. Jack Devine, a former top C.I.A. clandestine officer who helped run the covert war against the Soviet Army in Afghanistan in the 1980s, said his record showed that he was “not exactly a cream puff” when it came to advocating secret operations.

But he warned that the safeguards introduced after Congressional investigations into clandestine wars of the past — from C.I.A. assassination attempts to the Iran-contra affair, in which money from secret arms dealings with Iran was funneled to right-wing rebels in Nicaragua known as the contras — were beginning to be weakened. “We got the covert action programs under well-defined rules after we had made mistakes and learned from them,” he said. “Now, we’re coming up with a new model, and I’m concerned there are not clear rules.”

Cooperation and Control 
 
The initial American strike in Yemen came on Dec. 17, hitting what was believed to be a Qaeda training camp in Abyan Province, in the southern part of the country. The first report from the Yemeni government said that its air force had killed “around 34” Qaeda fighters there, and that others had been captured elsewhere in coordinated ground operations.

The next day, Mr. Obama called President Saleh to thank him for his cooperation and pledge continuing American support. Mr. Saleh’s approval for the strike — rushed because of intelligence reports that Qaeda suicide bombers might be headed to Sana — was the culmination of administration efforts to win him over, including visits by Mr. Brennan and Gen. David H. Petraeus, then the commander of military operations in the Middle East.

The accounts of the American strikes in Yemen, which include many details that have not previously been reported, are based on interviews with American and Yemeni officials who requested anonymity because the military campaign in Yemen is classified, as well as documents from Yemeni investigators.

As word of the Dec. 17 attack filtered out, a very mixed picture emerged. The Yemeni press quickly identified the United States as responsible for the strike. Qaeda members seized on video of dead children and joined a protest rally a few days later, broadcast by Al Jazeera, in which a speaker shouldering an AK-47 rifle appealed to Yemeni counterterrorism troops.
“Soldiers, you should know we do not want to fight you,” the Qaeda operative, standing amid angry Yemenis, declared. “There is no problem between you and us. The problem is between us and America and its agents. Beware taking the side of America!”

A Navy ship offshore had fired the weapon in the attack, a cruise missile loaded with cluster bombs, according to a report by Amnesty International. Unlike conventional bombs, cluster bombs disperse small munitions, some of which do not immediately explode, increasing the likelihood of civilian causalities. The use of cluster munitions, later documented by Amnesty, was condemned by human rights groups.

An inquiry by the Yemeni Parliament found that the strike had killed at least 41 members of two families living near the makeshift Qaeda camp. Three more civilians were killed and nine were wounded four days later when they stepped on unexploded munitions from the strike, the inquiry found.

American officials cited strained resources for decisions about some of the Yemen strikes. With the C.I.A.’s armed drones tied up with the bombing campaign in Pakistan, the officials said, cruise missiles were all that was available at the time. Drones are favored by the White House for clandestine strikes because they can linger over targets for hours or days before unleashing Hellfire missiles, reducing the risk that women, children or other noncombatants will fall victim.

The Yemen operation has raised a broader question: who should be running the shadow war? White House officials are debating whether the C.I.A. should take over the Yemen campaign as a “covert action,” which would allow the United States to carry out operations even without the approval of Yemen’s government. By law, covert action programs require presidential authorization and formal notification to the Congressional intelligence committees. No such requirements apply to the military’s so-called Special Access Programs, like the Yemen strikes.

Obama administration officials defend their efforts in Yemen. The strikes have been “conducted very methodically,” and claims of innocent civilians being killed are “very much exaggerated,” said a senior counterterrorism official. He added that comparing the nascent Yemen campaign with American drone strikes in Pakistan was unfair, since the United States has had a decade to build an intelligence network in Pakistan that feeds the drone program.
In Yemen, officials said, there is a dearth of solid intelligence about Qaeda operations. “It will take time to develop and grow that capability,” the senior official said.

On Dec. 24, another cruise missile struck in a remote valley called Rafadh, about 400 miles southeast of the Yemeni capital and two hours from the nearest paved road. The Yemeni authorities said the strike killed dozens of Qaeda operatives, including the leader of the Qaeda branch in Yemen, Nasser al-Wuhayshi, and his Saudi deputy, Said Ali al-Shihri. But officials later acknowledged that neither man was hit, and local witnesses say the missile killed five low-level Qaeda members.

The next known American strike, on March 14, was more successful, killing a Qaeda operative named Jamil al-Anbari and possibly another militant. Al Qaeda’s Yemeni branch acknowledged Mr. Anbari’s death. On June 19, the group retaliated with a lethal attack on a government security compound in Aden that left 11 people dead and said the “brigade of the martyr Jamil al-Anbari” carried it out.

In part, the spotty record of the Yemen airstrikes may derive from another unavoidable risk of the new shadow war: the need to depend on local proxies who may be unreliable or corrupt, or whose agendas differ from that of the United States.

American officials have a troubled history with Mr. Saleh, a wily political survivor who cultivates radical clerics at election time and has a history of making deals with jihadists. Until recently, taking on Al Qaeda had not been a priority for his government, which has been fighting an intermittent armed rebellion since 2004.

And for all Mr. Saleh’s power — his portraits hang everywhere in the Yemeni capital — his government is deeply unpopular in the remote provinces where the militants have sought sanctuary. The tribes there tend to regularly switch sides, making it difficult to depend on them for information about Al Qaeda. “My state is anyone who fills my pocket with money,” goes one old tribal motto.

The Yemeni security services are similarly unreliable and have collaborated with jihadists at times. The United States has trained elite counterterrorism teams there in recent years, but the military still suffers from corruption and poor discipline. 

It is still not clear why Mr. Shabwani, the Marib deputy governor, was killed. The day he died, he was planning to meet members of Al Qaeda’s Yemeni branch in Wadi Abeeda, a remote, lawless plain dotted with orange groves east of Yemen’s capital. The most widely accepted explanation is that Yemeni and American officials failed to fully communicate before the attack.

Abdul Ghani al-Eryani, a Yemeni political analyst, said the civilian deaths in the first strike and the killing of the deputy governor in May “had a devastating impact.” The mishaps, he said, “embarrassed the government and gave ammunition to Al Qaeda and the Salafists,” he said, referring to adherents of the form of Islam embraced by militants.

American officials said President Saleh was angry about the strike in May, but not so angry as to call for a halt to the clandestine American operations. “At the end of the day, it’s not like he said, ‘No more,’ ” said one Obama administration official. “He didn’t kick us out of the country.”

Weighing Success 
 
Despite the airstrike campaign, the leadership of Al Qaeda in the Arabian Peninsula survives, and there is little sign the group is much weaker.

Attacks by Qaeda militants in Yemen have picked up again, with several deadly assaults on Yemeni army convoys in recent weeks. Al Qaeda’s Yemen branch has managed to put out its first English-language online magazine, Inspire, complete with bomb-making instructions. Intelligence officials believe that Samir Khan, a 24-year-old American who arrived from North Carolina last year, played a major role in producing the slick publication.

As a test case, the strikes have raised the classic trade-off of the post-Sept. 11 era: Do the selective hits make the United States safer by eliminating terrorists? Or do they help the terrorist network frame its violence as a heroic religious struggle against American aggression, recruiting new operatives for the enemy?

Al Qaeda has worked tirelessly to exploit the strikes, and in Anwar al-Awlaki, the American-born cleric now hiding in Yemen, the group has perhaps the most sophisticated ideological opponent the United States has faced since 2001.

“If George W. Bush is remembered by getting America stuck in Afghanistan and Iraq, it’s looking like Obama wants to be remembered as the president who got America stuck in Yemen,” the cleric said in a March Internet address that was almost gleeful about the American campaign.

Most Yemenis have little sympathy for Al Qaeda and have observed the American strikes with “passive indignation,” Mr. Eryani said. But, he added, “I think the strikes over all have been counterproductive.”

Edmund J. Hull, the United States ambassador to Yemen from 2001 to 2004, cautioned that American policy must not be limited to using force against Al Qaeda.

“I think it’s both understandable and defensible for the Obama administration to pursue aggressive counterterrorism operations,” Mr. Hull said. But he added: “I’m concerned that counterterrorism is defined as an intelligence and military program. To be successful in the long run, we have to take a far broader approach that emphasizes political, social and economic forces.”

Obama administration officials say that is exactly what they are doing — sharply increasing the foreign aid budget for Yemen and offering both money and advice to address the country’s crippling problems. They emphasized that the core of the American effort was not the strikes but training for elite Yemeni units, providing equipment and sharing intelligence to support Yemeni sweeps against Al Qaeda.

Still, the historical track record of limited military efforts like the Yemen strikes is not encouraging. Micah Zenko, a fellow at the Center for Preventive Action at the Council on Foreign Relations, examines in a forthcoming book what he has labeled “discrete military operations” from the Balkans to Pakistan since the end of the cold war in 1991. He found that these operations seldom achieve either their military or political objectives.

But he said that over the years, military force had proved to be a seductive tool that tended to dominate “all the discussions and planning” and push more subtle solutions to the side.
When terrorists threaten Americans, Mr. Zenko said, “there is tremendous pressure from the National Security Council and the Congressional committees to, quote, ‘do something.’ ”
That is apparent to visitors at the American Embassy in Sana, who have noticed that it is increasingly crowded with military personnel and intelligence operatives. For now, the shadow warriors are taking the lead.


Muhammad al-Ahmadi contributed reporting from Yemen.

This article has been revised to reflect the following correction:

Correction: August 22, 2010




An article last Sunday about the Obama administration’s shadow war against Al Qaeda and its allies in roughly a dozen countries gave an outdated affiliation in some editions for Micah Zenko, who in a forthcoming book looks at what he calls “discrete military operations” from the Balkans to Pakistan since the end of the cold war. Mr. Zenko is a fellow at the Center for Preventive Action at the Council on Foreign Relations; he is no longer a scholar at the Kennedy School of Government at Harvard.

This article has been revised to reflect the following correction:

Correction: August 29, 2010



An article on Aug. 15 about the Obama administration’s secret counterterrorism operations overseas described incorrectly a recent strike in northern Africa that was cited as an example of coordination with allies. The strike in question, on July 22, was carried out by French and Mauritanian troops near the border between Mauritania and Mali; it was not a French strike in Algeria.



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