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Petraeus read a September 2 column by David Ignatius, a columnist for The Washington Post and the author of several well-crafted spy novels. He had spent many hours with Ignatius, a skilled reporter who traveled to Iraq, Afghanistan and other hot spots regularly, often with senior military, including Petraeus.

But what was this? Petraeus read an unwelcome headline, “A Middle Way on Afghanistan?” Ignatius trotted out the line that this could be “Obama’s Vietnam.” He cited the difficulties the British Empire had had despite “all its troops, wealth and imperial discipline.” But worse, Ignatius took a swipe at Petraeus’s counterinsurgency strategy. “There is little hard evidence that it will work in a country as large and impoverished as Afghanistan. Even in Iraq, the successes attributed to counterinsurgency came as much from bribing tribal leaders and assassinating insurgents.” Obama’s decision on Afghanistan would amount to a “roll of the dice.”

Petraeus was incredulous. In the fight for the hearts and minds of the American public—and the president—the message war was a deadly serious competition. The best way to counter Ignatius was to call the competition, so Petraeus phoned another Post columnist, Michael Gerson. He later claimed he was unaware that Gerson had been the chief speechwriter for President George W. Bush and the celebrated author of some of Bush’s most saber-rattling post-9/11 speeches.

Rebutting Ignatius’s critique, Petraeus told Gerson that adding troops for “a fully resourced, comprehensive counterinsurgency campaign” was the only way. There was no guarantee, he said, the war strategy “will work out even if we apply a lot more resources. But it won’t work out if we don’t.” In no uncertain terms, Petraeus was saying the war would be unsuccessful if the president held back on troops.

Obama and several of his staffers were furious. It angered Obama that Petraeus was publicly lobbying and prejudging a presidential decision. Bush’s former speechwriter must be a go-to guy for Petraeus, already suspect as a “Bush General.” As far as Obama was concerned, there were two times in recent history when a president faced major decisions on war—LBJ in 1965 when the Vietnam generals asked for escalation and 2003 when President Bush decided to invade Iraq. Both presidents had failed to drill down into the reasoning, the alternatives and the full consequences. Obama was determined not to repeat that mistake, and a preemptive strike in the public relations war by General Petraeus was distressing.

Denis McDonough read the Gerson column and understood the president’s frustration. He thought of how much easier it had been to maintain message consistency in the presidential campaign, where there were fewer players in the know and everyone was united by the goal of electing Obama. McDonough e-mailed Colonel Erik Gunhus, Petraeus’s spokesman, to express his irritation. Strategy and resource issues were precisely what the president wanted to debate and consider. It was not helpful to have the combatant commander pontificating in a newspaper about what the strategy must be and the certainty of defeat without the addition of a lot more troops.

Petraeus figured all presidents had a protective inner circle. Before Petraeus had appeared on Sunday morning TV shows, Axelrod participated in a conference call to help shape what the general would say. The suggestions by Obama’s senior adviser were often unsophisticated and political. Petraeus told one of his senior aides that he disliked talking with Axelrod, whom he called “a complete spin doctor.”

The general felt as though he had been relegated to the bench by the president. Use me, Petraeus wanted to tell Obama. Use me. Make me part of the team. At one point, he had told Emanuel, “Rahm, I want to win. I can be your lead sled dog here.”

“Yeah, okay,” Emanuel said. “We’re all in this together.”

Geoff Morrell, the Pentagon spokesman, weighed in after the Gerson piece, telling Petraeus to stay quiet. The White House was upset because it looked like the generals were trying to box in the president. Morrell asked to be the military’s single point of contact for all media interviews, effectively forbidding Petraeus from appearing on the Sunday morning television talk shows anymore. So Petraeus went to ground, but in his ongoing back-channel dialogue with Senator Lindsey Graham he hinted that the South Carolina Republican and some other pro-military senators ought to weigh in publicly.

On the evening of Saturday, September 12, Vice President Biden sat on Air Force Two, studying his notes about Afghanistan and Pakistan. The vice president had flown to Los Angeles to raise funds at a Beverly Hills luncheon for Senator Barbara Boxer and, separately, eulogize two firefighters who had died in the recent California wildfires.

Joining him was Tony Blinken, his national security adviser, so that they could prepare for the first of several three-hour NSC sessions to discuss and debate the McChrystal assessment. Gates had proposed the meetings. The first one was scheduled for the next morning.

Biden had spent five hours hashing out an alternative to McChrystal that he dubbed “counterterrorism plus.” Instead of a troop-intensive counterinsurgency, the plan focused on what he believed was the real threat—al Qaeda. Counterterrorism put an emphasis on shutting down terrorist groups by killing or capturing their leaders. Biden thought al Qaeda could be deterred from returning to Afghanistan without having to embark on the costly mission of protecting the Afghan people.

Al Qaeda, he reasoned, would always take the path of least resistance and not come back to its former home as long as:

1. The U.S. maintained at least two bases—Bagram and Kandahar—so Special Operations Forces could raid anywhere in the country;

2. The U.S. had enough manpower to control Afghan airspace, and the enemy was nowhere close to contesting that;

3. Human intelligence networks inside Afghanistan provided targeting information to Special Operations Forces; and

4. The CIA’s elite, 3,000-Afghan-strong Counterterrorism Pursuit Teams (CTPT) could move freely.

Afghanistan only had to be a slightly more hostile environment for al Qaeda than Pakistan (“one Predator tougher”) for them to choose not to return.

Biden was sold on counterterrorism plus. Obama needed a guide. The president had a mere four years in the Senate. Biden had 35. He believed the military could not push him around, but they could roll an inexperienced president. Biden went to Obama.

You know these guys, the president said. Go after it. “Push.”

Obama later explained to me that he had encouraged the vice president to be an aggressive contrarian. “I said, Joe, I want you to say exactly what you think. And I want you to ask the toughest questions you can think of. And the reason is, is because I think the American people are best served and our troops are best served by a vigorous debate on these kinds of life-or-death issues. I wanted every argument on every side to be poked hard. And if we felt a little give there, we wanted to keep on pushing until finally you hit up against something that was incontrovertible and something that we could all agree to. And so in that sense I think Joe served an enormously useful function.” At no point, Obama said, did he believe that Biden pushed too hard.

“Personal Observations on Afghanistan,” Jones wrote as a heading in his black Moleskine-style notebook. The national security adviser was composing his ideas and questions for the review sessions.

“We’re about to change the strategy before evaluating the product of the first decision.” That was the crux of the problem. It was crazy to not evaluate the results of the Riedel strategy before making a shift, but here they were.

“Is Pakistan the main effort? Really, should it be?”

In terms of endgame, Jones wrote, “What is good enough?” Outright victory might be out of reach, so they had to find something else. In other words, don’t let the perfect be the enemy of the good. Was the U.S. military aware of what good enough meant?

The U.S. had been playing an unsuccessful game of “Mother may I” with both Karzai in Afghanistan and the Pakistani leadership. The U.S. had a right to make some demands, given the investments made in lives and money. Presidents Bush and Obama had been embarrassingly tolerant for too long.

Jones was sure that the best answers, if there were any, would come from a review that adhered to the formal NSC system. Procedure and protocol mattered to the retired Marine general.

Citing the botched attempt to close Guantánamo, he had once told Obama, “Every time you go outside the box—the National Security Council process—we lose.” The president seemed to agree.

“Thanks for coming in on a Sunday morning,” Obama said as he gathered a small group of his most senior national security team in the Situation Room on September 13. All the main players were there, except for Petraeus, who had not been invited, and CIA Director Panetta, who DNI Blair had kept out.

Burrowed in the windowless room and its black leather seats, the group was missing part of a warm fall day. Obama had read McChrystal’s 66-page classified assessment, which said that without more forces the war “will likely end in failure” in the next 12 months. It was an unnerving declaration, but he was far from convinced.

“We have no good options here,” the president said, making it clear he would not automatically accept the general’s, or anyone’s, solution. “We need to come to this with a spirit of challenging our assumptions. I’m a big believer in continually updating our analysis and relying on a constant feedback loop. Don’t bite your tongue. Everybody needs to say what’s on their mind. Lots of young men and women out there are making tremendous sacrifices.”

The president turned the meeting over to Dr. Peter R. Lavoy, the deputy for analysis in the Office of the Director of National Intelligence. An expert on nuclear proliferation, Lavoy speaks Hindi, Urdu and French and has a Ph.D. in political science from Berkeley. He is the DNI’s top authority on Pakistan. Such meetings usually begin with an intelligence update.

“Al Qaeda’s embattled,” Lavoy said. The drone attacks and other counterterrorist operations had bin Laden and his organization hurting, beleaguered but not yet finished. Al Qaeda has a tenuous foothold in Afghanistan—20 to 100 people there at the most. So Pakistan instead has become the epicenter of their fight. And because of its weakened condition, al Qaeda has grown more dependent on local extremist groups for support.

“They’re the leech riding on the Taliban, and strength for the Taliban gives strength to the leech riding on it,” Lavoy said. For example, the Haqqani network, a Taliban ally with compounds in Pakistan’s tribal areas, is very important to al Qaeda’s survival. While the Taliban and al Qaeda have different goals, their senior leadership—meaning Mullah Omar and bin Laden—probably remains pretty close. But the Taliban now needs al Qaeda less than al Qaeda needs the Taliban.

The Taliban does see itself as winning in Afghanistan, which gives a boost to al Qaeda, Lavoy continued. And as long as the Taliban believes it’s winning, it also has little incentive to make peace with the Karzai government. Taliban leader Mullah Omar has a good, adaptive command structure out of Quetta, Pakistan. The whole Taliban insurgency is designed to outlast the coalition of U.S. and international troops.

Lavoy’s boss, DNI Dennis Blair, stepped in to explain why the Pakistani government had not been more helpful in rooting out the different Islamic groups.

“Pakistan thinks about the U.S. role in Afghanistan in the context of its relationship with India,” Blair said. It was the cliché that Pakistan’s obsession with its mortal enemy, India, caused the nation to harbor terrorists.

Obama then recognized Biden, who offered a prelude to his thinking. “There’s a fundamental incoherence in the strategy” for dealing with Pakistan, the vice president said. “What Pakistan doesn’t want, as a matter of faith, is a unified Afghan government that is led by a Pashtun sympathetic to India” like Karzai. So for Pakistan, supporting the Taliban “is a hedge against that.

“But our policy is designed to strengthen a Karzai government and to wipe out the Taliban,” Biden said, indicating that it was impossible to win over the Pakistanis completely. “My hunch,” he added, “is that the Pakistanis have concluded that we cannot afford to leave” Afghanistan now. Essentially, American policy reinforces Pakistani hedging in a self-defeating cycle, causing Pakistan to aid the Afghan insurgency that the U.S. is trying to beat.

Gates then brought attention back to Lavoy, asking, “What’s the impact on al Qaeda central in the region as compared to its position globally?”

“Al Qaeda is coming under pressure worldwide,” Lavoy said, “so to justify its leadership role in the global jihad, it’s aligning itself with this nexus of militant groups and its role” against the U.S. and NATO forces in the region “as the defining piece of its mission.”

“Given it’s on the defensive in the wider struggle,” asked the president, reframing Lavoy’s argument, “they can and are using our presence in Afghanistan as a motivation and ideological underpinning of its effort. True?”

“That’s true,” Lavoy answered. “Al Qaeda’s goals, in order, are: one, preserve the safe haven in the FATA, and, two, advance the goals of global jihad by taking the fight to Afghanistan and Pakistan. So to do that, they question the legitimacy of the Karzai government.”

Lavoy continued, “Pakistanis would prefer a Taliban government to a broad-based multiethnic government [in Afghanistan]. As long as they think the Taliban can come back, they will not break with the Taliban. They currently believe the circumstances are such that the Taliban can come back.”

The analysis seemed to endorse the conclusion in McChrystal’s assessment that the Taliban held the momentum.

Obama had questions he wanted answered more concisely. Can al Qaeda be defeated and how? Do you need to defeat the Taliban to defeat al Qaeda? Can a counterinsurgency strategy be effective in Afghanistan given the capacities of the Afghan government? What can we realistically expect to achieve in the next few years? What presence do we have to have in Afghanistan in order to have an effective counterterrorism platform?

Secretary Clinton then offered an overview of the diplomatic and political context. It would likely be September or early October, she reported, before the Afghan elections were finalized. “Karzai is currently at 54 percent. Nevertheless, there might be enough fraud that legitimacy would definitely be in question.” If enough ballots were eliminated for fraud, Karzai might fall below 50 percent and there would be a runoff election. A second round of voting, she said, “by the same token, is also fraught with peril.

“The second question,” Clinton said, “is whether we should be associated with an effort toward reconciliation.” Could something be worked out with the Taliban? “What would we demand of it, and who will have a role in it?” Which Taliban should the U.S. negotiate with? Moderates? Mullah Omar? What role would Karzai have?

Holbrooke interjected, “The Karzai meeting this morning was hot.”

Eikenberry added, “It’s starting to dawn on him that this is a very different American administration.” Abdullah Abdullah, Karzai’s main rival in the elections, he added, “won’t go quietly but he does recognize privately that he would lose in a second-round” runoff election.

Gates introduced the McChrystal assessment. “The elements associated with the strategic decision you put in place earlier are only now coming into focus,” he said, referring to the March Riedel report, the decisions and the president’s speech. “Resources are just getting into place. McChrystal’s assessment is the first chance to review that.” Gates said McChrystal’s troop request needed more work, so it had not yet arrived.

McChrystal is proposing four big changes, Gates said, “Accelerate the ANSF [Afghan National Security Forces] training. Prioritize governance. Enhance programs for reconciliation and reintegration. And there’s got to be a geographic concentration of our efforts.”

The “geographic concentration” line caught Jones’s attention. He thought the military leaders were talking as though the entire Afghanistan War could be won in the south. Jones believed that was just flat wrong, but he did not interrupt.

“I believe the strategy is the right one, but it is under-resourced,” Gates continued. “It’s premature to discuss resources until we have a very clear sense of how we tie the McChrystal approach to al Qaeda, how we deal with corrupt and predatory Afghan governance, how we change the subject from nation building to capacity building and how we address Pakistani unwillingness to take on the Pakistani Taliban,” also known as the TTP.

Mullen then briefed the group on the McChrystal assessment from a pack of PowerPoint slides entitled “Sunday Small Group, 13 September 2009.” He covered the four points from the report that Gates had made, adding, “Governance is at least the same threat, if not the greater threat, than the Taliban themselves.”

When Mullen concluded, Biden was the first to speak. “This isn’t an easy call. The military’s done a hell of a job. But a nationwide, reinforced counterinsurgency will only expand costs and demand extra resources. So is there not a more efficient way to go about this?”

They then attempted to address the question: Who are al Qaeda’s extremist allies? That was the language in the Riedel review that had been open to interpretation.

“I think we have to focus on the threats to us and our allies and our interests,” the president said, emphasizing a narrow definition, “not just any piece of any insurgency in Afghanistan.”

“That’s right,” Gates said, “we have to focus on those groups that have the capacity to threaten us, our interests, our overseas presence, or our allies.”

“I want to say six things,” Biden said. He was learning to edit himself, but he still could be verbose and some in the room seemed to tense up. During one President’s Daily Brief in the Oval Office, Biden apparently had disagreed with an intelligence conclusion and merely, without elaboration, shouted out one word—“Wrong!”—and left it at that. He could not be that abrupt this morning.

“This is the most consequential decision we’ll make,” Biden said, “so we need to make sure we understand the ramifications, or other concerns. Do we have the balance right between Afghanistan and Pakistan?” He noted that the allocation of “resources was currently 30:1—Afghanistan to Pakistan.” Shouldn’t the focus be Pakistan? he asked.

“Two, what is the most effective way to do what this says?” he asked, pointing to his copy of the McChrystal assessment.

“Three,” Biden asserted, moving from questions to firm declarations, “the premise of the counterinsurgency strategy is flawed. There’s a balloon effect. We squeeze it, and it pops out somewhere else. Are we prepared to go to other countries where al Qaeda can pop up?

“Four, the prospects for counterinsurgency are dim. We are in our seventh year of this war, and even when successful, counterinsurgency takes seven to 10 years, historically. Even if it were doable, McChrystal says he needs the will and ability to provide for the Afghan people by, with and through the Afghan government. They would need an effective government presence in 40,200 villages in Afghanistan.

“Fifth point, the alternative isn’t to leave.” The real alternative was “counterterrorism plus,” a shift to an emphasis on Pakistan, al Qaeda and training more Afghan forces.

“Six,” the vice president said, “it’s not that the counterterrorism plus strategy has been tried and failed. We’ve not tried a fully resourced anything in Afghanistan, let alone one that does exactly what I say we need to do.”

Biden then moved to the morning’s intelligence briefing, disputing the claim that al Qaeda and the Taliban were so intertwined and so intermingled that the success of one meant the success of the other.

“No, they’re actually very distinct,” Biden said. “We’re assuming that if al Qaeda comes back into Afghanistan, where it wasn’t, it would be welcomed by the Taliban. Is that a correct assumption? We have no basis for concluding that.”

The vice president then talked about the hierarchy inside the Taliban. It is not a “monolith,” he said. There are several levels of organization. It had hard-core believers at a senior level, at best 5 or 10 percent, who need to be defeated. Then there was a middle group of people, perhaps 15 or 20 percent, who had different reasons for being committed. Maybe they were more persuadable, but it wasn’t clear. And about 70 percent of the Taliban were foot soldiers, who were only there because it was a way to put food on the table or to deal with getting foreigners out of the country. These were illiterate, uneducated kids who were given a rifle and told to point it in that direction.

“We have to differentiate,” Biden said. And the major differentiation is that the hard-core Taliban leaders—the ones causing the most headaches in Afghanistan—are all in Pakistan.

Bottom line, Biden said, it didn’t necessarily matter what they did in Afghanistan. “If you don’t get Pakistan right, you can’t win,” he said, addressing the president. If you do what McChrystal wants and adopt his strategy, “You own this war.”

“I already own it,” Obama said.

What was unsaid, what everyone knew, was that a president could not lose—or be seen to be losing—a war.

After a pause, Obama attempted a summary. “We’re going to have to work through five areas,” he said, posing a series of unanswered questions. “What are the opportunity costs, given the finite resources?” Were other national interests being overlooked because of the focus on this? It was a radical change from Bush, who was all in, win at all costs. Obama was proposing they consider other national priorities. “Is pursuing a broader counterinsurgency the best way to advance our core goal?” And because that goal is defeating al Qaeda in order to protect the homeland, did we really have to win a civil war in Afghanistan?

“Two, we’ve got a very real problem with corrupt governance, and I don’t see how you get around that if you go with counterinsurgency.

“Three, Pakistan. I’m not persuaded that executing counterinsurgency in Afghanistan gets Pakistan to move in the right direction. How do we change Pakistan’s calculus? It’s not even clear that Pakistan would accept our increased resources.” Obama said he thought some of the points the vice president had raised were valid.

“Four, how do we get good intel and targeting with a smaller presence on the ground?

“Five, when we approached the new strategy, we said we’d need a year. Where did this accelerated timetable come from?” The strategy from the Riedel review was supposed to be assessed after a full year—in March 2010—but it was only September. This sudden sense of urgency was unexpected. “Why do we have to make an accelerated decision?” he asked.

It was the core question and no one answered him.

Gates addressed the question of opportunity costs from a military perspective. “Given the drawdown in Iraq,” he said, “we could increase troop numbers in Afghanistan without impacting the dwell time at home.” Dwell time refers to time at home base.

Admiral Mullen concurred.

“We’re going to need another session,” Obama said. “We’re just scratching the surface here. This discussion has also clarified our core goal, highlighting the fact that we have done a disservice to McChrystal by not making that very clear to him.” The Strategic Implementation Plan (SIP) was the origin of that problem. At Gates’s urging, it said that goal was to “defeat” the insurgency, the broadest and most difficult task.

“Is there any confidence in our capacity, in a three-year time frame?” the president asked. That was how much time was left in his presidential term. Anybody who has any confidence in our capability to build anything of consequence in three years has not really explained their case, he said. It was a direct shot at the military.

“What happened in Iraq?” he asked of counterinsurgency’s most recent test case. Was the surge plus the Sunni Awakening, when tribes left the insurgency and joined the government, a strategic decision? There had been sufficient infrastructure in Iraq for that decision to have coherence, he said. “We have to make sure that there’s similar infrastructure in Afghanistan. I do recognize that it would be difficult to execute a counterterrorism plus strategy without a good foothold in Afghanistan. That intuitively makes sense, because without it you’re not going to get good intelligence.”

Referring to the next session, he said, “I want to start with Secretary Clinton on the Pakistan/al Qaeda question, and have a discussion about a realistic end state in that.”

The president then doled out homework assignments. This meeting had concentrated on the McChrystal assessment. He wanted to take a step back.

“We’re going to begin with interests,” Obama said, “and then figure out what it is we want to accomplish, how we’re going to do it and eventually get to resources. We don’t want to talk about troops initially.”

I don’t even want to see the troop request that McChrystal’s preparing, Obama said. It would only obscure the debate he wanted to have about their real “interests.”

Holbrooke left the Situation Room thinking that some of the real issues had not been discussed at all. The March Riedel report was flawed. Riedel had presented it in a one-hour Air Force One meeting alone with the president. No one else had been there—not Jones, not Donilon, not Emanuel, not himself. There was no note taker. Four or five people should have been on that plane and in the meeting.

In the Bush administration one of the problems had been the very private sessions that Bush had with Vice President Cheney, who could present his arguments and whisper in the president’s ear. Cheney’s ideas did not have to be tested, and they were given undue influence.

Holbrooke blamed Jones, who he thought was weak and not proactive enough in protecting the president. He was not the counterweight to Gates, Mullen and Petraeus he was supposed to be.

More importantly, Holbrooke believed the Riedel report and the Sunday meeting had not acknowledged a central truth: The war—or the American role in the war—would not end in a military victory, but nearly all the focus had been on the military. There had been little discussion of reconciliation—how the warring parties could be brought together diplomatically. That might be far off, but it had to be planned. How could the Taliban insurgents be lured off the field? Maybe it was a fantasy. But they had to sincerely try.

The Saudis were already acting as secret intermediaries with elements of the Taliban, but the White House was not seriously engaging the issue. This was the only end for the war in Holbrooke’s estimation. How could they not at least consider it?

Holbrooke largely agreed with Biden. He saw the vice president emerging as the administration’s George Ball, the deputy secretary of state who had opposed the Vietnam escalation. But the length of Biden’s presentation undermined his message, Holbrooke told others.

Like Biden, Holbrooke believed that even if the Taliban retook large parts of Afghanistan, al Qaeda would not come with them. That might be “the single most important intellectual insight of the year,” Holbrooke remarked hours after the first meeting. Al Qaeda was much safer in Pakistan. Why go back to Afghanistan, where there were nearly 68,000 U.S. troops and 30,000 from other NATO counties? And in Afghanistan, the U.S. had all the intelligence and surveillance capability, plus the capability to dispatch massive ground forces, not just Special Operations Forces but battalions of regular troops and the CIA’s 3,000-man pursuit teams.

Astonishingly to Holbrooke, that key insight had neither been in Riedel’s report, nor had it been discussed that Sunday morning. Where was the no-holds-barred debate? The president had told them not to bite their tongues. Holbrooke had to bite his because he worked for the secretary of state, who was unsure of what course to recommend. But where were the others?

Petraeus had not been invited to attend the White House meeting. Instead, the CentCom commander was in Tampa, conducting a halftime reenlistment ceremony at the Buccaneers-Cowboys football game. He thought his exclusion from the meeting was ridiculous. Petraeus was the combatant commander in Afghanistan and Pakistan and recognized as the father of modern counterinsurgency—the strategy under review.

He received a synopsis the next day, Monday, September 14, from General Lute, who had attended. They spoke at 8:30 A.M. for half an hour on a secure personal Tandberg video. Petraeus agreed that Pakistan was important but not all-important. What they did in Pakistan also depended on what they did in Afghanistan.

For Petraeus, war was about initiative and momentum. Regaining the initiative on the ground in Afghanistan was crucial, as was regaining the initiative inside the Situation Room. With one session down, he believed that Mullen was all in on McChrystal’s approach and that Gates was increasingly persuaded.

In the message war, Petraeus had allies outside the administration who shared his beliefs and trusted his judgment. On Monday, September 14, a long op-ed appeared in The Wall Street Journal written by Senators Graham, Lieberman and McCain. Under the headline “Only Decisive Force Can Prevail in Afghanistan,” the senators said they would stand with Obama if he gave McChrystal what the general said he needed. They did not disclose that McChrystal had told them he would need seven to eight brigades. Echoing Petraeus, they wrote, “More troops will not guarantee success in Afghanistan, but a failure to send them is a guarantee of failure.”