A Bing Maps satellite image of what appears to be a remote air strip in Saudi Arabia. (Screenshot of bing.com)

Four years ago, as a new al-Qaeda affiliate in Yemen was proving itself a potent adversary, the Obama administration made plans to attack it with airstrikes just as the United States had been doing to the terrorist network’s core in Pakistan.

But this time, the White House decided there would be a key difference: The strikes in Yemen would be carried out by the U.S. military, not the CIA.

Two years later, in mid-2011, a mysterious construction project began to emerge in the Saudi desert, an elongated compound with a ribbon of concrete running parallel to the ridgelines of the surrounding dunes. CIA drones were about to enter the skies over Yemen after all.

The change was driven by a number of factors, including errant strikes that killed the wrong people, the use of munitions that left shrapnel with U.S. military markings scattered about target sites and worries that Yemen’s unstable leader might kick the Pentagon’s planes out.

But President Obama’s decision also came down to a determination that the CIA was simply better than the Defense Department at locating and killing al-Qaeda operatives with armed drones, according to current and former U.S. officials involved in the deliberations.

Even now, as the president plans to shift most drone operations back to the military, many U.S. counter­terrorism officials are convinced that gap in capabilities has not been erased.

The issue has taken on heightened significance as Obama imposes new rules on U.S. counter­terrorism operations that are designed to give the Pentagon the lead in the targeted killing of terrorism suspects overseas, reducing and perhaps eventually replacing the role of the CIA.

In a major speech Thursday, Obama talked of the seductive appeal of a weapon whose precision and secrecy offer a shield from accountability, saying it can “lead a president and his team to view drone strikes as a cure-all for terrorism.” Turning to Pentagon drones was described as a way to move the campaign out of the shadows of covert operation.

But even those who agree with the decision said it may prove more difficult for Obama to dismantle the CIA’s drone program than it was to shutter its secret prisons, because of the agency’s expertise as well as circumstances that at times enable the CIA to operate in places off-limits to the Defense Department.

“You have to go into this with some concern,” a former senior U.S. counter­terrorism official said of the plan. “It didn’t work before. Will it work this time?”

Sen. Dianne Feinstein (D-Calif.), chairman of the Senate Intelligence Committee, raised a related concern earlier this year when word of the administration’s plan began to surface.

Feinstein said that she had seen the CIA “exercise patience and discretion specifically to prevent collateral damage” and that she “would really have to be convinced that the military would carry it out that well.”

Critics contend that, despite Obama’s claims of accuracy, the CIA has killed hundreds of innocent civilians, along with as many as 3,000 militants, most of them low-level fighters, in Pakistan and Yemen.

A Yemeni activist, Farea al-Muslimi, testified before Congress last month that the campaign has been indiscriminate, causing anti-U.S. sentiment to surge. “What radicals had previously failed to achieve in my village, one drone strike accomplished in an instant,” he said. “There is now an intense anger and growing hatred of America.”

Since 2009, when Obama became president, the United States has carried out more than 360 strikes in Pakistan and Yemen, according to data compiled by the Long War Journal Web site. The CIA has accounted for the vast majority of those, including all 293 in Pakistan, where only the agency flies armed drones.

The drone campaign in Pakistan began under President George W. Bush and escalated after Obama took office. But from the outset, Obama administration officials expressed discomfort with the fact that an intelligence service had absorbed a lethal mission that had traditionally been the responsibility of the military.

In an interview in late 2010, a senior Obama administration official stressed that the CIA was running the drone campaign in Pakistan mainly because the agency was first to develop the technology after the Sept. 11, 2001, terrorist attacks and because Pakistan’s government insisted on secrecy so that it could deny any U.S. operations on its soil.

“It has been in Yemen a different story, a different history, a different evolution,” the official said, making clear that the administration regarded the CIA campaign as an anomaly and saw lethal operations as the province of the military.

The U.S. military’s elite Joint Special Operations Command was already flying drones over Yemen from a base in Djibouti on the Horn of Africa. Using drones, warships and conventional aircraft, JSOC had already launched a flurry of strikes against al-Qaeda targets.

The first had come on Dec. 17, 2009, just three days after al-Qaeda in the Arabian Peninsula was designated as a terrorist organization by the U.S. government. That initial attack, which involved missiles fired from a U.S. warship, was inauspicious.

The strike killed 14 al-Qaeda operatives but also 35 women and children, including several who later died after stepping on unexploded cluster munitions, according to Amnesty International and other outside accounts.

A week later, on Christmas Day, AQAP attempted a strike of its own when a Ni­ger­ian trained and equipped by the group boarded a transatlantic flight for Detroit with a bomb hidden in his underwear. The plot might have killed hundreds if the device hadn’t failed to detonate.

The JSOC airstrikes intensified after the plot, but costly mistakes and misses piled up.

In May 2010, the United States thought that it had a senior al-Qaeda fighter in its sights but killed Jabir al-Shabwani, a deputy governor of a Yemeni province who reportedly was meeting with militants in an attempt to get them to make peace.

The most consequential miss came a year later, when JSOC drones and Harrier jets fired a series of shots at Anwar al-Awlaki, a U.S.-born cleric who had become a senior AQAP figure and was seen as a driving force in the organization’s plots against the United States.

The pickup in which Awlaki was traveling emerged intact from two strikes, barreling through a remote stretch of Shabwa province. A third strike finally destroyed the truck, but only after Awlaki had switched vehicles and escaped.

In Washington, U.S. counter­terrorism officials were dismayed.

“You’re only going to get so many shots at high-value targets, and you have to make them count,” the former senior U.S. counter­terrorism official said.

“I never fully understood why they struggled so much,” the former official said, referring to the Pentagon’s problems. “Of all the pieces, the kinetic piece at the end was what they should have been good at.”

By then, the secret CIA base in Saudi Arabia was beginning to take shape.

U.S. and Saudi officials said the kingdom had been pushing the United States to ramp up its involvement in neighboring Yemen, particularly after an August 2009 attempt by a suicide bomber to kill Saudi counter­terrorism official Muhammed bin Nayef.

Two years later, when White House counter­terrorism adviser John Brennan, then-CIA Director Leon Panetta and other U.S. officials presented a plan to build a drone base in Saudi Arabia, the royal family didn’t flinch, according to U.S. and Middle Eastern officials involved in the discussions.

The idea was a provocative one. A founding grievance for al-Qaeda was the presence of U.S. military ­forces in the Islamic Holy Land in the 1990s. Now the United States was about to install its signature counter­terrorism weapon, the symbol of a campaign that had inflamed anti-American sentiment among millions of Muslims.

Saudi officials were undaunted and even conjured a plausible cover story. If the facility were discovered, the kingdom would say it was a delivery station for construction materials needed to build a fence along the Saudi-
Yemen border.

“There was no worry or thinking of blowback,” a Middle Eastern official said. “There was the urgency of turning around a situation in Yemen that was very dangerous.”

The contours of the base blend into the desert topography so inconspicuously that the facility is nearly impossible to detect from wide-angle satellite images. But magnifications reveal a lengthy runway and clamshell hangars used at other airstrips by the United States to house drones.

The Saudi government imposed conditions, including full authority over the facility and assurances that there would be no U.S. military personnel on site. The operation would be run by the CIA and Saudi intelligence, who for years had jointly operated a fusion center in Riyadh.

Feeding targeting intelligence to JSOC drones was not seen as a valid option, in part because doing so would require military approvals that could bog down a process requiring split-second decisions, officials said.

“The military’s culture is very uncomfortable with someone not in the chain of command handing them a target package and saying, ‘Hit this,’ ” said Jeremy Bash, who served as a senior aide to Panetta at the Pentagon and the CIA.

The first CIA flights began in August 2011. Six weeks later, Awlaki was killed in a CIA strike.

U.S. officials cited a list of factors that contribute to the agency’s lethal efficiency. Among them is its expertise at penetrating terrorist groups through networks of informants, and the expertise of officers and analysts who tend to stay in their assignments longer than their military counterparts. The head of the agency’s Counter­terrorism Center has been in the job for more than seven years, a time frame in which JSOC’s command has changed hands three times.

Bash said that those advantages are not insurmountable but that “for DOD to become the best in class at these types of operations will require it to invest significant resources in training, capabilities and new doctrines.”

A second senior administration official said drone operations have been precise and accurate, regardless of whether they were carried out by the CIA or military. “This is not about one agency versus another,” said the official, who, like others, spoke on the condition of anonymity to discuss the classified operations. “This is about strengthening a proven national framework for continued success against our terrorist enemies.”

In many ways, the push to restrain the CIA is driven by the perceived costs of its counter­terrorism emphasis, concern that the agency’s focus on lethal operations has diverted it from its traditional intelligence-gathering and analysis mission.

Brennan, who became director in March, was a driving force in drafting Obama’s new guidelines. But Brennan was also among the senior officials who initially favored putting JSOC in charge of the campaign in Yemen before turning to the CIA.

Officials noted that the guidelines establish a “preference” for the military to handle drone strikes but don’t rule out a continuing role for the CIA.

The number of U.S. strikes in Yemen rose to 42 last year but they have tapered off since. After a flurry of attacks in January, there have been only three. The latest, on May 18, reportedly killed four militants but no senior operatives and was carried out by the CIA.