WASHINGTON -- In the skies above Yemen, the Pentagon's armed drones have stopped flying, a result of the ban on U.S. military drone strikes imposed by the government there after a number of botched operations in recent years killed Yemeni civilians. But the CIA's drone war in Yemen continues.
In Pakistan, the CIA remains in charge of drone operations, and may continue to be long after U.S. troops have left Afghanistan.
And in Jordan, it is the CIA rather than the Pentagon that is running a program to arm and train Syrian rebels -- a concession to the Jordanian government, which will not allow an overt military presence in the country.
Just over a year ago John O. Brennan, the CIA's newly nominated director, said at his confirmation hearing that it was time to refocus an agency that had become largely a paramilitary organization after the Sept. 11 attacks toward more traditional roles carrying out espionage, intelligence collection and analysis. And in a speech last May in which he sought to redefine U.S. policy toward terrorism, President Barack Obama expanded on that theme, announcing new procedures for drone operations, which White House officials said would gradually become the responsibility of the Pentagon.
But change has come slowly to the CIA.
"Some might want to get the CIA out of the killing business, but that's not happening anytime soon," said Michael A. Sheehan, who until last year was the senior Pentagon official in charge of special operations and now holds a distinguished chair at West Point's Combating Terrorism Center.
A number of factors -- including bureaucratic turf fights, congressional pressure and the demands of foreign governments -- have contributed to this delay. At the same time, Brennan is also facing a reckoning for other aspects of the CIA's role at the forefront of the secret wars the United States has waged since 2001.
The declassification of a scathing report by the Senate Intelligence Committee about the agency's detention and interrogation program will once again cast a harsh light on a period of CIA history Brennan has publicly disavowed. The U.S. Justice Department has been drawn into a dispute between the agency and the committee, and is looking into a charge by Sen. Dianne Feinstein, the committee's chairwoman, that the agency broke the law by monitoring computers of committee staff working on the report.
Before taking charge of the CIA last March, Brennan had spent four years as Obama's top counterterrorism adviser, a job that put him in charge of the targeted killing operations that became a signature of the Obama administration's approach to terrorism.
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It also made Brennan -- who before working for Obama had spent 25 years at the CIA -- a powerful influence on a president with no experience in intelligence.
U.S. officials said that in that role Brennan repeatedly cautioned Obama that the CIA's counterterrorism mission threatened to attenuate the agency's other activities, most notably those of penetrating foreign governments and analyzing global trends. During his confirmation hearings, Brennan obliquely criticized the performance of U.S. spy agencies in providing intelligence and analysis of the Arab revolutions that began in 2009, and said the CIA needed to cede some of its paramilitary role to the Pentagon.
"The CIA should not be doing traditional military activities and operations," he said.
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Now, Brennan is in charge of a counterterrorism apparatus that has steadily grown in budget, manpower and influence for more than a decade. While officials said that Brennan has pushed for more resources to counter traditional adversaries like Russia and China, as well as newer threats like cyberwarfare, the agency's Counterterrorism Center, known as the CTC, remains a powerful force both inside the agency and on Capitol Hill.
"I think that most of the CIA is behind the changes, but the CTC community has grown dramatically since 9/11 and is fighting to keep its turf," Sheehan said. "And, they've been somewhat successful in that regard, especially with the drone programs."
Influential lawmakers from both parties have fought to protect the CIA's role in the drone wars and prevent the proposed shift of the bulk of drone operations to the Pentagon.
Both Feinstein and Rep. Mike Rogers of Michigan, chairman of the House Intelligence Committee, have urged Brennan to push back against the White House policy announced last May, citing what they regard as the Pentagon's poor performance in lethal operations outside of Iraq and Afghanistan.
A number of bungled drone strikes carried out by the Joint Special Operations Command in Yemen led the government there in recent months to temporarily ban drone strikes by the military, which are launched from a U.S. base in Djibouti.
Officials said that the ban, not previously reported, came after a military drone strike in December killed a number of civilians who were part of a wedding procession in a desolate region south of Yemen's capital, Sanaa.
Meanwhile, the CIA continues to wage its own drone war in Yemen, launching the unmanned planes from Saudi Arabia.
In Pakistan, where the CIA also is in charge of the drone program, the pace of strikes has declined sharply, and there have been none since the government in Islamabad formally entered peace talks with the Pakistani Taliban, according to the Bureau of Investigative Journalism, a group that tracks drone strikes.
But U.S. officials said that the drone program there could continue for years, and Pakistan's government has long insisted that it be run by the CIA, not the U.S. military.
This was one of the terms of the deal reached a decade ago between the Bush administration and Pervez Musharraf, then the president of Pakistan, who said he would allow armed drone strikes in the country's tribal areas only if they were conducted as a CIA covert action and not acknowledged by either country. For Pakistan to agree to any changes in this arrangement, the United States would most likely have to agree to integrating Pakistan's military into the drone operations.
A White House spokeswoman said there had been "no change in policy" since Obama's speech last May announcing changes to targeted killing policy.
"The plan is to transition to these standards and procedures over time, in a careful, coordinated and deliberate manner," said Caitlin Hayden, the spokeswoman. "I'm not going to speculate on how long the transition will take, but we're going to ensure that it's done right and not rushed."
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It was during the string of revolts across the Arab world several years ago that concerns first surfaced that the years of focus on targeting terrorists had undermined the CIA's ability to forecast and analyze global events. In Egypt, the agency had few sources beyond Omar Suleiman. The country's intelligence chief and one of the agency's closest partners in the Middle East, Suleiman was not about to give the CIA an honest assessment of the fragility of President Hosni Mubarak's government.
Responding to a written question from the Senate Intelligence Committee during his confirmation process, Brennan said that "with billions of dollars invested in CIA over the past decade, policymaker expectations of CIA's ability to anticipate major geopolitical events should be high."
"Recent events in the Arab world, however, indicate that CIA needs to improve its capabilities and its performance still further."
The previous year, a panel of advisers had warned Obama that U.S. spy agencies were overly focused on paramilitary operations, at the expense of intelligence collection in the Middle East, China and other locations.
Philip D. Zelikow, a former member of the panel, known then as the President's Intelligence Advisory Board, called the report a "very broad critique" of the CIA, and said that the agency should not be carrying out drone strikes.
"I think these kind of military operations over the long haul are best confined to the Department of Defense," Zelikow said.
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In recent weeks, the heads of several intelligence agencies have faced accusations from lawmakers that U.S. spies and analysts were caught by surprise when Russia swiftly annexed Crimea. Particular criticism has been reserved for the Defense Intelligence Agency, responsible for intelligence collection about foreign militaries, for concluding that Russian troop movements near the Ukraine border were unlikely to lead to an invasion of the Crimean Peninsula.
Even if the CIA eventually does give up the work of firing missiles and dropping bombs in far-flung regions of the earth, Brennan insists that its counterterrorism mission will endure.
"Despite rampant rumors that the CIA is getting out of the counterterrorism business, nothing could be further from the truth," the CIA director said during a speech last month at the Council on Foreign Relations.
The agency's covert action authorities and relationships with foreign spy services, Brennan said, "will keep the CIA on the front lines of our counterterrorism efforts for many years to come."
By MARK MAZZETTI
The New York Times