John Brennan, Obama's CIA Chief Nominee, Could Restrain the Agency

John Brennan, the president's counterterrorism chief and now his nominee to head the CIA, has spent his career in the darkest corners of the terror wars—and he has a grim public reputation to match. A massively built man with a labored gait and deep-set eyes that can appear menacing, Brennan has time and again been assailed by liberals and civil libertarians. They accuse him of having supported torture at the Bush-era CIA and, more recently, of having orchestrated Obama's legally dubious war of drone strikes and targeted killings. They point out that, in his current job, Brennan presides over a process so secretive that the public knows little about how many people have been killed, let alone how many of them have been innocent civilians.

If you listen to people inside the White House, however, you will hear about an entirely different Brennan. Yes, they will say, he is indeed deadly serious about hunting terrorists. (David Axelrod has said that he slept better knowing Brennan didn't sleep.) But he also passionately supports civil liberties and wants to fight terrorism within a framework of law. In fact, far from being seen as an unbridled hawk, Brennan is widely viewed by colleagues as an often-moderating influence in the war on terror. His very presence in the West Wing, administration insiders say, is a daily affirmation of one of Obama's central creeds in his war on al Qaeda: that America's strength is rooted in its values. "There's no one who cares more about the security of this country and going after people who are bent on killing American citizens," says Director of National Intelligence James Clapper. "But at the same time, John is a pillar of courage when it comes to insisting on American values and the rule of law."

Next week Brennan, 57, will briefly step out of the shadows as the Senate takes up his confirmation to be CIA director. Effectively, the hearing will revolve around one of Washington's biggest unsolved riddles: Is John Brennan a hawk? A dove? A staunch civil libertarian? A man with enormous amounts of innocent blood on his hands? Or some semi-contradictory combination of the above?

To answer these questions, it helps to understand what has taken place inside the White House over the past four years. Upon assuming control of the war on terror, Obama and Brennan inherited a program of targeted killing with fuzzy criteria and shifting procedures. Together, they have groped toward a clearer framework for when the United States should carry out targeted killings—"rules of the road," as one White House official put it. Their partnership—arguably unique in the annals of American war—recently culminated in the production of a highly classified document known as "the playbook," which Obama hopes will guide his administration as well as those of future presidents. The advent of the playbook was a signal development in the 12-year-old war on terror. But it was a long, arduous road for the two men to get to this point—one that reveals much about Brennan's worldview and about how he might run the CIA.

It all began four years ago when Brennan and Obama met for the first time in Chicago. The newly elected Obama was looking for a CIA director; Brennan was a 25-year veteran of the agency who had served both at Langley and overseas, including a tour as station chief in Saudi Arabia. He spoke fluent Arabic and had a subtle feel for Muslim societies. (Brennan pronounces "al Qaeda" with the soft guttural of the Arabic he learned as a student at the American University in Cairo.)

During the meeting, both men talked about the need for a "surgical" approach in dealing with terrorism, according to a source familiar with their conversation. Brennan likened it to a doctor treating cancer. "You need to attack the metastasizing disease without destroying the surrounding tissue," he said. Obama, worried about blowback, explained that he did not want to use military force as a "blunt instrument." The conversation led them directly to what would become the new administration's weapon of choice due to its vaunted precision and lethality: weaponized pilotless aircraft, or drones.

The two men bonded quickly—and given their backgrounds and worldviews, it shouldn't have been a surprise. Schooled as a constitutional lawyer, Obama's instincts tilt toward using the law to protect the innocent. Brennan's views were shaped by his Roman Catholic upbringing and occasional forays into just war theory. He, too, has a legal bent of mind, perhaps the product of his Jesuit education and the many years he spent as a CIA analyst. "John's told me that he thinks there are a lot of similarities between lawyers and analysts," says a former colleague, explaining Brennan's affinity for attorneys. "He's very careful, logical, and detail-oriented." (Brennan—who is rarely impressed with the perks of his powerful position—was thrilled to be seated next to Antonin Scalia at last year's state dinner for the British prime minister.)

But Obama's fast bond with Brennan was not enough to get him the CIA job. As soon as Brennan's name was floated, the liberal blogosphere lit up with accusations that he had been involved in the Bush administration's torture program while working as a top aide to then-CIA director George Tenet after Sept. 11. Though much about his role during the aftermath of 9/11 remains murky, Brennan has said he did, in fact, object to harsh interrogation techniques; and after he left government in 2005, he publicly equated waterboarding with torture. But Brennan's critics were not to be mollified. Obama got cold feet, and Brennan withdrew his name.

His supporters say the episode stung, but also emboldened him to become a more forceful voice in support of civil liberties and the rule of law. "It strengthened his resolve," says David Boren, a former chairman of the Senate Intelligence Committee and a co-chair of President Obama's Intelligence Advisory Board.

Brennan, whose grave countenance masks a warm and generous side ("the scowl on his face turns into a smile pretty quickly," says one colleague), settled for a job as Obama's chief adviser on counterterrorism and homeland security. Working from a windowless bunker in the basement of the West Wing, Brennan acted as Obama's guide to the shadowy world of intelligence and counterterrorism. But, according to administration sources, the two men did not just talk about how to kill terrorists; they also talked about how to pursue the enemy without further compromising America's international reputation, already eroded by torture and Guantánamo. And befitting their lawyerly instincts, they would, time and again over the years, search for ways to establish rules, standards, and constraints—to ensure that the war on terror was ultimately governed by laws, not men. "These past four years have brought out John's natural desires to dive more deeply into the legalities and ethical nature of these counterterrorism challenges," says Michael Leiter, who worked closely with Brennan as the former head of the National Counterterrorism Center. "These weren't questions he had to grapple with in the same way at the CIA."

Obama and Brennan found themselves grappling with the real-world implications of such questions almost immediately. On Jan. 23, 2009, the CIA launched its first attacks on Obama's watch. One of them mistakenly killed an innocent tribal elder in Pakistan and much of his family. It was Brennan who delivered the grim news to Obama. Three days into his presidency and Obama was presiding over the death of innocent Muslims. Brennan, according to two senior intelligence officials, called over to the CIA to let them know the president was not happy.

Later, at a tense Situation Room meeting, Obama learned for the first time about a controversial practice known as "signature strikes": the targeting of groups of "military-age males" who bear certain "signatures" or defining characteristics associated with terrorism, but whose identities aren't known. It was, participants at the meeting recall, a concept Obama had a hard time wrapping his mind around. Brennan backed the CIA tactic, explaining to the president that after nearly a decade of operating in Pakistan, the agency's spies knew the territory intimately, minimizing the likelihood of mistakes. But, administration officials say, he also urged the president to supervise the CIA more closely and to tighten its targeting standards.

It was a pattern that would repeat itself over the next four years: Brennan the pragmatist was perfectly willing to deal death to suspected terrorists. Yet he was simultaneously mindful of the need to establish constraints on America's program of targeted killings. "The thing that John could do better than anyone else was explain sensitive operations to the president, make him comfortable with them, and help him manage them," says Leiter.

Nowhere were the subtleties in Brennan's worldview more obvious than in Yemen, a country he had long personal ties to from his days as CIA station chief in Saudi Arabia. The CIA operated mostly in Pakistan, which was viewed by the administration as an extension of the Afghan theater. But the agency wasn't the only wing of the government involved in targeted killings. The military had its own lethal program, and it was operating in countries, including Yemen, where the United States was not officially at war.

Obama, who was worried about mission creep, not to mention operating on the margins of the law, decreed that he would be the final decision maker for the military's kill or capture operations. Meanwhile, Brennan supervised a process designed to keep the military program in check. Targeted killings undertaken by the Pentagon would be subjected to vigorous interagency vetting. Dozens of officials from across the national security bureaucracy would gather on a secure video conference to hash out the security, policy, legal, and humanitarian considerations. The sessions were run by the Pentagon but once a decision to go forward with a strike was made, it was Brennan who brought the recommendation to Obama. Together they made the crucial life and death decisions.

Not surprisingly, Obama developed a bit of gallows humor about Brennan. When he'd turn up unannounced at the Oval Office, the president would sometimes arch an eyebrow and remark, "Uh-oh, this can't be good." Still, as macabre as the encounters could be, they ultimately acted as one more constraint on the targeted killing program. Sometimes, they resulted in a death sentence; but sometimes they resulted in a life spared or an attack canceled.

Yemen came to the forefront of the war on terror after Christmas 2009, when Umar Farouk Abdulmutallab came close to blowing up a commercial airliner and killing more than 300 people. The plot was quickly traced back to al Qaeda in the Arabian Peninsula (AQAP), the group's affiliate in Yemen, and a charismatic American-born Yemeni cleric named Anwar al-Awlaki. Obama and Brennan saw Awlaki as a perilous threat to the United States and wanted more aggressive counterterrorism operations in Yemen. But how they handled the situation was emblematic of their complicated approach to these matters.

The military wanted to conduct broad-based signature strikes in the country. But Obama was worried about getting embroiled in a domestic conflict—and he and Brennan said no. Then, in the spring of 2011, with bin Laden dead, the military again proposed massive signature strikes in Yemen, thinking that the time was right to deliver a knockout blow to al Qaeda and its most dangerous affiliate, AQAP.

But Obama and Brennan, fearful of getting sucked into a wider war, remained opposed. Brennan employed his best bureaucratic weapon to brush back the generals: Obama. He told the president that it was time to make an "unequivocal statement," which would go out through the "interagency," that he was opposed to such signature strikes. Soon thereafter, at one of his weekly counterterrorism briefings—the so-called Terror Tuesday meetings—Yemen was on the agenda. When one of the president's military advisers made a reference to the ongoing "campaign" in Yemen, Obama, according to two participants in the meeting, abruptly cut him off. There's no "campaign" in Yemen, he said sharply, reminding the general that the goal there was to protect the homeland by going after members of al Qaeda, not to get involved in a civil war.

The military did not give up easily. By late 2011, according to counterterrorism officials, Brennan was increasingly worried that the Pentagon was attempting end-runs around the White House. Recommendations for larger strikes kept showing up on his desk. So Brennan blew up the decision making process and pulled it into the White House. He tasked the Counterterrorism Security Group, made up of officials from across the national security bureaucracy, to work through individual targeting "nominations." Meanwhile, Brennan brought in the National Counterterrorism Center to put together profiles of potential targets. He didn't want the agencies that had their fingers on the trigger to be in charge of the intelligence. Many in the Pentagon saw this as a bureaucratic power grab by Brennan. But it may also have been a way for him to rein in the targeted killing program.

While they devoted much effort to restraining the military and the CIA in Yemen, Brennan and Obama also remained quite pragmatic about the situation—and more than willing to use violence. In September 2011, the CIA (working with the Pentagon) carried out a highly controversial drone strike that killed Awlaki—controversial because, while Awlaki was an evil man, he was also an American citizen. Then, in the spring of 2012, with Yemen falling into chaos and AQAP gaining more and more territory, Yemeni officials—with whom Brennan had close ties going back to his days as a CIA station chief in the region—beseeched Brennan to help. The Yemeni Army was collapsing under the brutal assault; soldiers were being crucified and beheaded by the jihadis. By April 2012, Brennan and Obama finally relented and permitted signature strikes in the country.

Those who defend this decision point out that it would have been a catastrophe for U.S. security if significant parts of the country had fallen to AQAP, which was intent on attacking the American homeland. Yet some inside the administration were critical. Says one senior administration official of Brennan's history in Yemen: "He responded to the personal appeals because he has a long history with these guys." In other words: Brennan's lawyerly preference for rules and constraints may sometimes have taken a backseat to emotion.

Obama and Brennan were not always in agreement when it came to the war on terror. There have been times when Brennan was willing to be more muscular than the president. On one such occasion, Obama had approved a target in Yemen but rejected another. But in mid-operation the military realized it had a clean shot at the suspected militant whom Obama had crossed off the list, according to a senior military official with knowledge of the operation. With little time to spare, Brennan, at the military's urging, persuaded Obama to reverse his decision. The target was soon dead.

One senior counterterrorism official who has worked closely with Brennan says that while he often counsels restraint, he is not gun-shy. And he is not afraid to steer others toward the conclusion that someone ought to die. Sometimes it's the way he frames a question in a meeting. "Is there anyone here who doesn't think this guy's a bad guy?" he might say, according to the source.

At the same time, Brennan has also occasionally been to the left of the president. He was disappointed that the White House did not push back harder against congressional opposition to closing Guantánamo—and he let the president know it.

Moreover, on other contentious security issues, Brennan has routinely taken a civil liberties–minded view. He vigorously supported prosecuting 9/11 mastermind Khalid Sheikh Mohammed in federal court and defended law enforcement administering Miranda warnings to suspected terrorists. Last year, Brennan took the unusual step of publicly informing Congress about the administration's lethal operations in Yemen and Somalia. He also began giving speeches that gingerly laid out some of the legal theories behind the administration's drone program, and urged others to do the same.

And then there is "the playbook"—an ambitious attempt to create explicit rules and procedures for when lethal force is justified. The initiative began more than a year ago. It is highly detailed and lays out, for example, criteria for the so-called disposition-matrix, which prescribes whether terrorist suspects should be killed, captured, or dealt with in some other way. Embedded in the document are the legal authorizations for pursuing the enemy away from conventional battlefields in places like Yemen, Somalia, and now Mali—a crucial check on a war without defined boundaries. The playbook also toughens the standard for when a targeted killing is justified. Simply being a threat to "United States interests," for example, no longer meets the threshold. That standard is too elastic, according to officials who have been involved in writing the new rules. And the document makes finely grained distinctions about where one must be in the chain of command of a terrorist organization to be targetable. A driver or cook, who can be easily replaced, may not represent the kind of unique threat that would warrant lethal action. A bomb maker, on the other hand, would.

The process of assembling the playbook has been contentious. One of the most drawn-out bureaucratic battles was over the role the president should play in targeting. The military pushed hard to take the commander in chief out of the process. Once the president approves a battle plan in a particular country, individual targeting decisions should be left up to the regional commanders, they argued. The CIA agreed. At one point they seemed to have won the argument, and their proposed change became part of the playbook. But after a furious counteroffensive by the State Department and other agencies, the status quo was restored.

In addition, when Brennan decided to create a common decision making process for both the military and the CIA, Langley pushed back. Since the inception of its drone program, targeting decisions have been made inside the CIA with little or no input from other branches of the government. Under Brennan's plan, the agency would have been subject to the same interagency vetting process that the military now goes through. In the end, the CIA seems to have won a partial victory: according to The Washington Post, the agency's operations in Pakistan, where it fires most of its drone strikes, will be exempted from the playbook for a year. Still, with Brennan soon to arrive at the CIA, one wonders if that victory will be short-lived.

Before the downfall of David Petraeus, Brennan was preparing to leave gov- ernment. He was ready to move on after four grueling, stress-inducing years in one of Washington's most high-stakes positions. "I've run out of runway," he told colleagues. Few understand the stresses of the job as well as Richard Clarke, who held it during the Clinton and Bush administrations. "It's truly a 24/7 job," he says. "You can never get drunk or tie one over. It's an invisible anchor."

But when Obama asked him to take over the CIA, Brennan couldn't say no. And that, despite the loudly voiced objections to his nomination, might end up being good news for the civil-liberties crowd. "John embodies the principle that aggressive counterterrorism and first principles can exist side by side," says a former administration official who worked closely with him. Yes, improbable as it may seem, John Brennan—a bona fide hawk who believes deeply in targeted killing and has spent the past four years ordering people executed—may end up doing more than anyone else to rein in the war on terror.