On his first day in office, President Barack Obama will head to the situation room for a video conference with his most important commander, General David Petraeus. If the conversation is chilly, it is not just the awkwardness of virtual chatting. Obama and Petraeus have a history. While Obama has called for withdrawing U.S. forces from Iraq, Petraeus oversaw the deployment of more than 30,000 additional troops. To win support from the left, Obama postured as a skeptic of the general's Iraq strategy during congressional hearings. Meanwhile, Petraeus has emerged as something of a hero to the right--and, despite his protestations, might someday run for president as a Republican.

But, more than any campaign rhetoric or past slights, the relationship between the general and his commander-in-chief will hinge on much larger questions about Barack Obama and the war on terrorism.

And, while it's easy to dismiss the conservative critique of Obama's foreign policy as a politically motivated caricature, you can see why McCain supporters have tried to tag him as a latter-day Jimmy Carter. During the primaries, Obama talked about the war on terrorism with the fastidiousness of a civil libertarian--emphasizing the constraints that he would impose on our military and CIA and rarely mentioning specific methods for prosecuting it. He has, for instance, talked extensively about closing the Guantánamo Bay prison and ending the policy of extraordinary rendition.

There are arguably many moral and strategic reasons for this agenda. But the insights gleaned from the counterinsurgency in Iraq and seven years of fighting Al Qaeda across the world also yield harsher lessons. American national interests often demand collaboration with security forces, militias, and tribal leaders who don't conform to our highest ideals. What's more, a key plank of the Petraeus strategy in Iraq is to isolate and shrink the pool of irreconcilable insurgents. That means in practice paying off former bomb-makers, torturers, and terrorists to entice them to join the fight against Al Qaeda--and these are, needless to say, not the types to fret over the nuances of the Geneva Conventions. Or, as one former Sunni insurgent turned ally in Fallujah told The Washington Post, "We never tortured anybody. Sometimes we beat them during the first hours of capture."

If you read the fine print of Obama's policy papers and talk with his advisers and examine their careers, you'll find something surprising about how an Obama administration would view this dark side of the war on terrorism. Far from eschewing alliances with unsavory proxies, these ties are essential to Obama's plans for destroying Al Qaeda. As he has put it, the United States must develop the "partnerships we need to take out the terrorists." Obama hasn't fully fleshed out what he means, but his advisers have some ideas. They told me that he would deepen cooperation with Pakistan's government and military and Somalia's transitional federal government in their battles with Al Qaeda--and that, while opposed to the troop surge, he applauds the partnership between the U.S. military and Iraqi tribal leaders that helped turn the tide in the fight against Al Qaeda there.

So, even though Obama and Petraeus have rhetorically gone in diametrical directions in the last year, they have actually converged on substance. In important ways, an Obama approach to the global insurgency of Al Qaeda mirrors Petraeus's counterinsurgency in Iraq.

Before unpacking the Obama view of the war on terrorism, let's dismiss the comparisons to Jimmy Carter. A bit of a refresher course in the horrors of the late 1970s: Jimmy Carter pledged to enshrine human rights as a central value in U.S. foreign policy. That was an admirable goal, but Carter didn't just inject human rights into U.S. foreign policy; he allowed it to rule policy, no matter the implications for the fight against communism. During the Carter era, the United States cooled its relations with vital client states like the Shah's government in Iran and the Somoza regime in Nicaragua, even as they fought for their lives. The locus classicus of this critique was, of course, Jeane Kirkpatrick's Commentary essay, "Dictatorships and Double Standards," where she excoriated the Carter administration for its studied neutrality as pro-American autocrats fell to Marxist-Leninist revolutionaries. She concluded that Carter's foreign policy was incapable of distinguishing between real democratic activists and would-be totalitarians who cloaked their ambitions in the rhetoric of democratic self-determination. "Liberal idealism need not be identical with masochism, and need not be incompatible with the defense of freedom and the national interest," she wrote.

Does her critique apply to Barack Obama, too? That's what John McCain has, in essence, alleged. But to understand why this charge won't stick--and to understand the intellectual DNA of the Obama approach to counterterrorism--you need to review the careers of Richard Clarke and Rand Beers.

Both Clarke and Beers are lifelong national security bureaucrats who left the Bush administration in protest of the Iraq war. Both have offered private advice to Obama and might well hold top posts in his war cabinet. Clarke helped draft the campaign's counterterrorism strategy, and Beers contributed ideas for his August 1, 2007 counterterrorism speech. Both also have the trust of the party's antiwar base and have, in many ways, articulated the Democratic Party's most substantive critique of Bush's war on terrorism.

From some of their criticism of the Bush administration, you might think them soft-power squishes. But, during their careers, they have never expressed much hesitation about working with proxy armies with less than admirable human rights records. During the Clinton administration, Beers served as the assistant secretary of state for international narcotics and law enforcement affairs, a bureau known as "drugs and thugs." In that post, he helped conceive Plan Colombia, which has, over the last eight years, funneled about $5.5 billion to the country's military. Much of that has been spent combating the Revolutionary Armed Forces of Colombia (FARC), which has funded its Marxist- Leninist rebellion by presiding over a vast drug empire.

In many ways, the program was a great success. Today, the FARC is nearly defeated, and the civil war in that country is over. But Plan Colombia worked in part because Beers was prepared to assist a national army that worked closely with pro-government death squads--and, for that reason, Plan Colombia provoked the ire of Vermont Senator Patrick Leahy and the left wing of the Democratic Party. Beers takes criticism of this brand of alliance seriously but considers it surmountable. He told me that such alliances require that the United States conditions its assistance: "We are prepared to work with you, but you are going to have to change your stripes. You are going to have to operate in a fashion where that kind of behavior stops." Indeed, in the Colombian instance, there's strong evidence that Beers's plan also helped curb the worst excesses of America's military partners.

Clarke is a somewhat more familiar figure. During congressional testimony, he famously apologized for allowing September 11 to happen while serving as the National Security Council's terrorism czar. He left a long paper trail on Al Qaeda, including the "Delenda Memo" of 1998, which takes its name from the Latin word to "blot out" and was based on a more detailed strategy for regime change in Afghanistan. In both its goals and rhetoric, that strategy harkened back to the cold war. It spoke of "rollback," and, taking a page from the anti- communist strategy of the Reagan years, it called on the government to fight a proxy war against Al Qaeda and their Taliban hosts.

Like Beers's Plan Colombia, Clarke's approach placed the United States in bed with thugs. He proposed "massive support" to the anti-Taliban coalition that included the sadistic warlord Abdul Rashid Dostum, who would, in 2001, load thousands of Taliban fighters into sealed containers. When the captives pleaded for air, Dostum's men shot holes in the containers--and many of the prisoners therein. The strategy also called for covert assistance to the regime of Uzbek dictator-for-life Islam Karimov, who has allegedly ordered the boiling of his political opponents. Clarke told me that he and his staff knew that, if such alliances managed to neutralize the threat from Al Qaeda without a major attack, they would face political heat for their tactics: "Everyone would say we were crazy because the disaster never occurred."

Clarke and Beers in effect were drawing on a time-honored tradition of foreign policy that goes back to the Gurkhas: finding proxies to fight an enemy. It was a tradition for America that found its apotheosis in the Reagan Doctrine of the 1980s, which was defined by Charles Krauthammer as "unashamed American support for anti-Communist revolution," regardless of whether or not such support respected the sovereignty of communist states. It was a policy that manifested itself in U.S. support for the Nicaraguan Contras, Jonas Savimbi's insurgency in Angola, and the Afghan mujahedin. In a sense, the Reagan doctrine was a full-throated rejection of the Carter era. It was Kirkpatrick's Commentary essay put into practice. So here we arrive at the central irony of the charge that Obama will revive Carterism: The two most important architects of his counterterrorism policy came of age at the height of the Reagan Doctrine, and that thinking continues to inform their strategy.

Last November at a foreign policy forum in Portsmouth, New Hampshire, Obama said there may be "40,000 hard-core jihadists with whom we can't negotiate." He went on. "Our job is to incapacitate them, to kill them." In that spirit, he famously announced that he would strike terrorist bases in Pakistan if President Pervez Musharraf ever refuses to move on actionable intelligence against Al Qaeda--a threat that earned him the chastisement of John McCain, among others.

Of course, the opportunities for that kind of strike are rare and the diplomatic costs can be high. That's where we begin to see the interesting confluence that will likely emerge as the Obama Doctrine. His counterterrorism policy will bear the imprint of the Beers-Clarke experience in the national security apparatus. And that pedigree will be coupled with the lessons that David Petraeus has gleaned from Iraq. The result will likely be a combination of force and kindness. In the search for allies against Al Qaeda, the U.S. military will aggressively seek out allies among the tribes that co-mingle with the terrorists, as well as the police and intelligence agencies in those countries. Our military would try to pry them away from Al Qaeda by offering them money and basic infrastructure--and then send them into battle against the terrorists. But, at the same time, through that engagement, it would also attempt to instill practices that minimize the brutality and corruption of local police.

A good guide to what such an ambitious program would look like is Obama's plan to give frontline police and intelligence agencies $5 billion over three years through a "Shared Security Partnership Initiative." His campaign materials promise the plan will extend "from the remote islands of Indonesia to the sprawling cities of Africa."

Or take the Pakistan example. Richard Clarke envisions a policy that would pressure and entice the Pakistani military, which has been markedly reluctant to challenge jihadists, to use the same sorts of tactics that have flourished in Iraq: "The Pakistani army is not trained and equipped for counterinsurgency. One of the things we say is, 'We know you are reluctant to do this. But we would like to help you, give you military aid and create an ability to do this. '" As one of Obama's top foreign policy advisers, Susan Rice, puts it, "Obama will support efforts to encourage the legitimate leaders in Pakistan's tribal areas who seek to thwart extremism." (Rice made sure to add that the campaign believed the conditions in Anbar to be different than in the Pakistani frontier and that it was primarily the responsibility of the Pakistanis to root out terrorist safe havens in their sovereign territories.)

Both Clarke and Beers concede that this type of counterinsurgency necessitates keeping some unpleasant company. The Pakistani intelligence services, for instance, have an atrocious history of abetting Al Qaeda; tribal leaders who Obama would like to co-opt operate under prehistoric codes of justice. But the Obama program would attempt to cajole its partners into abandoning brutal tactics.

Clarke explains this as follows: "When you partner with people with unsavory records, it has to be consciously a temporary spate, partnering has to include fixing them, and they have to be genuinely willing to be fixed." In fact, this is the key difference between the Reagan doctrine and the Petraeus-Obama brand of counterinsurgency--where the Reagan doctrine placed its emphasis on blowing up bridges, Petraeus and Obama want to build them. Their program depends on winning the allegiances of local populations--a goal undermined, over the long run, by brutal tactics.

Susan Rice is tipped to be a senior figure in an Obama administration. Earlier this month, I sent her a handful of questions about counterterrorism policy. Her answers were filled with all the hedges and qualifications that you would expect in the middle of a campaign. She told me that Obama would eschew a "one size fits all approach" to fighting terrorism. "In some cases that may mean strong support for proxies (as in Anbar). In other places it may mean direct U.S. action. In others, it may mean relying more on an allied government or the international community." But there were several answers she provided that I found highly revealing. She described Obama's opinion of America's historic involvement with insurgency and counterinsurgency. She applauded the 1980s arming of the mujahedin resistance to the Soviets: "[S]upport for the Afghan resistance to Soviet aggression was the right decision in the 1980s." And she said that the Anbar Awakening was "responsible for much of the security progress we have seen in Iraq," though she insisted that Sunni militias must eventually be incorporated into state security forces. In light of some of the criticisms that have been lobbed in Obama's direction, those are pretty suggestive allusions.

Of course, the Obama counterterrorism policy is still a work in progress. As his recent zigzags illustrate, he still hasn't figured out his stance on some of the larger questions. But, in discussing his plans for Iraq, he has made one key admission: He will listen carefully to the advice of his generals. You can easily see how this will play out. Obama will enter office with a set of somewhat inchoate instincts about American power and the importance of outsourcing force. These instincts will mesh with the evolving thinking of his top commanders, who have also begun to realize the limitations of an overstretched army and the value of counter-insurgency. And that brings us back to the situation room on Obama's first day. If he and Petraeus can overcome whatever awkwardness lingers, they will discover a mind meld and an emerging doctrine-- a doctrine that looks a lot more like Ronald Reagan than Jimmy Carter.