Petraeus and Panetta: What Their New Roles Mean for the CIA and Defense Department

President Obama is expected to announce Thursday that he’ll nominate General David Petraeus, the commander of US forces in Afghanistan, as the next director of the Central Intelligence Agency. With that move, the CIA will have completed its decade-long conversion into a paramilitary organization, focused primarily on hunting and killing terrorists and insurgents and less on trying to make sense of the world for decision-makers in government.

The CIA has long been divided between its two main cultures: clandestine operations and analysis. The stock of the latter fell in the wake of disastrous intelligence judgments, mainly those preceding the 9/11 attacks and the invasion of Iraq. But it was already in decline in the aftermath of the Cold War, as Washington’s power structure came to rely less on secret intelligence and more on public information in the press.

Meanwhile, the clandestine service, which has by no means had clean hands in the war on terror, has carved out a central role fighting America’s enemies in the remote regions of the globe, largely via a not-so-secret campaign of drone strikes in Pakistan and on the Arabian Peninsula. As the CIA has gotten better at hunting down and killing people, it has come to look increasingly like a military outfit run by civilians. Petraeus’s ascendancy begins to make a lot more sense when you consider that the difference between CIA and military operations is getting less significant all the time.

While it’s not unheard of for a military officer to head the civilian intelligence agency (it has happened seven times), Petraeus brings an unparalleled understanding of counterterrorism operations on every significant battlefield in which US forces are now engaged. And that expertise redounds to the CIA’s operational side. President Obama has eclipsed his predecessor in the use of drone strikes, which have become so essential to the administration’s counterterrorism efforts that current CIA director Leon Panetta once called them “the only game in town.” The future of those strikes is now in question, and the military has by no means been an unwavering fan of the CIA’s methods. But for the purposes of his new job, Petraeus will face practically no learning curve on these matters when he takes over at Langley. (His confirmation by the Senate is virtually guaranteed.)

Panetta, who had almost no intelligence background when he took the job two years ago, will now move over to the Defense Department, replacing Secretary Robert Gates, himself a former CIA director. Having overseen the expansion of the drone campaign, Panetta now possesses an operational (read paramilitary) credential that he lacked when he joined the administration. There’s a clear path now from the CIA to the Pentagon. One could imagine Petraeus himself having eyes on the Defense Secretary’s job.

Some observers have pointed out that the reshuffling of Obama’s national-security team, which was long-anticipated and also includes some key diplomatic appointments, reflects a desire for continuity in the administration. And that’s clearly true. The President could have taken a bolder and far more politically risky tack by nominating Michèle Flournoy to replace Gates. Instead, he chose easily confirmable officials who are already up to speed.

But internally, within the highly institutionalized culture of the CIA, this changing of the decks is a historical turning point. Obama is heralding a new era for the agency, and he’s sending a clear signal that he values its fighting side more than its thinking side.

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Shane Harris