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Admiral Mullen appeared before the Senate Armed Services Committee for his confirmation hearings for a second two-year term as chairman on Tuesday, September 15, two days after the first strategy session. He had carefully drafted a three-page opening statement and gone over it with Navy Captain John Kirby, his public relations assistant. He would try to preempt any questions in the opening.

Knowing the sensitivity of the troop issue, Kirby had sent a copy of the statement to McDonough at the White House, drawing attention to the line that said McChrystal’s strategy of a properly resourced counterinsurgency “probably means more forces.”

As all nominees do, Admiral Mullen had promised to give the committee his honest conclusions and not hedge his testimony. It was not unusual for the Pentagon to give the White House a heads-up about what senior officials planned to tell Congress, but Kirby was effectively asking for approval.

McDonough okayed the statement. The “probably” made it ambiguous enough. More forces could be interpreted as the almost inevitable addition of more U.S. troops for training the Afghan army.

But when Obama heard about Mullen’s testimony, he let his staff know how unhappy he was. Mullen was publicly endorsing the McChrystal strategy. “The Taliban insurgency grows in both size and complexity,” he had told the senators. “That is why I support a properly resourced, classically pursued counterinsurgency effort.” Had Mullen ignored what Obama said just two days earlier? Had the president not told everyone, including Mullen, that none of the options looked good, that they needed to challenge their assumptions, and they were going to have four or five long sessions for debate? What was the president’s principal military adviser doing, going public with his preemptive conclusion? The chairman was poking his finger in the president’s eye.

Later that day around 6 P.M., Pentagon spokesman Geoff Morrell was waiting in the lobby outside the White House Situation Room when Emanuel and Tom Donilon emerged from the NSC principals meeting. They were furious.

The president is being screwed by the senior uniformed military, they told Morrell. The generals and admirals are systematically playing him, boxing him in.

Filling his rant with expletives, Emanuel said, “It’s bullshit that between the chairman and Petraeus, everybody’s come out and publicly endorsed the notion of more troops. The president hasn’t even had a chance!”

Morrell realized that Mullen could have ducked the controversy at his hearings with a simple feint: “My job is to be the principal military adviser to the president of the United States and secretary of defense, and I owe them my counsel first and privately before I offer it to you all. I am happy to come back at a later point and give you what I offered … but I don’t think it’s appropriate to share it with the committee before.”

Morrell concluded it was all part of Mullen’s “compulsion to communicate,” to enhance the prominence and stature of the chairman’s position, after it had been emasculated by his two predecessors in the Rumsfeld era. The chairman had a Facebook page, a Twitter account, YouTube videos and a Web site called “Travels with Mullen: Conversation with the Country.”

Mullen himself then stepped into the lobby and discovered that he was the topic of a heated powwow. Jones joined them.

Emanuel and Donilon attempted to tone down their approach by asking him, How are we supposed to deal with this? You did this, what should we say?

“It’s going to be the lead story on all the evening news,” Emanuel said. “It’s going to be double black headlines above the fold on every single newspaper.”

As they were standing there, McDonough passed by. Mullen looked at McDonough as if he, the NSC chief of staff, would come to his defense. But McDonough continued on without a word.

Mullen was surprised they were giving him hell. The fears about headlines were overblown. The White House knew in advance what he was going to say. No specific troop number was in his testimony. He had been as amorphous as he could be. At his confirmation hearing, he must tell the truth. And the truth was that he embraced the general notion of a counterinsurgency. “That’s what I believe.” What was his alternative?

Why use “probably”? Donilon asked pointedly. Wouldn’t “I don’t know” have been better?

Mullen let them seethe. “I just took it,” he said later.

“Mullen: More Troops ‘Probably’ Needed,” read the headline at the top of The Washington Post front page the next morning.

Afterward, Jones called Mullen to ask how he was doing.

“I don’t know, you tell me,” the admiral replied.

“Losing altitude,” Jones said.

Obama asked retired General Colin Powell, the former secretary of state and chairman of the Joint Chiefs, to come for a private meeting in the Oval Office on September 16. A nominal Republican, Powell had given Obama an important endorsement during the presidential campaign. Nearly 25 years older, Powell had 35 years in the U.S. Army, and many had thought he would be the first black president. But Powell had chosen not to run in the 1990s, even when his poll numbers had skyrocketed.

“It isn’t a one-time decision,” Powell told the president about Afghanistan. “This is the decision that will have consequences for the better part of your administration. Mr. President, don’t get pushed by the left to do nothing. Don’t get pushed by the right to do everything. You take your time and you figure it out.”

Also, don’t get pushed by the media, he advised. Take your time, get all the information you need and make sure you are absolutely comfortable with where you come down.

“If you decide to send more troops or that’s what you feel is necessary, make sure you have a good understanding of what those troops are going to be doing and some assurance that the additional troops will be successful. You can’t guarantee success in a very complex theater like Afghanistan and increasingly with the Pakistan problem next door.

“You’ve got to ensure that you’re putting this commitment on a solid base, and the base is a little soft right now,” he said, referring to Karzai and the widespread corruption in his government.

During this period, I had been conducting interviews for this book about what McChrystal’s classified assessment said. It was the basis for both Petraeus’s and Mullen’s controversial statements, yet no one outside of a tight-knit inner circle had actually read it. My sources said that McChrystal’s analysis addressed a devastating conundrum: eight years of war with little to no progress.

There is a popular impression that insiders with political motivations simply hand over sensitive documents to journalists, with reporters waiting at their desks to be used as the tools of someone else’s agenda. No one offered to leak or provide me a copy of the McChrystal assessment. Through several interviews, I developed an understanding that the assessment was filled with troubling news. I used each interview to try to pry out a little more.

In mid-September, after a nearly two-hour interview, I asked one person, “You’ve got a copy of the McChrystal report here?”

“Yeah, it’s on my desk,” was the answer, and that person photocopied the report for me.

The person put no restrictions on using the assessment, but the interview had taken place as part of the long-range research for this book. I did not get a chance to read the report until Friday night, September 18.

With a red pen in hand, I went through the 66-page confidential assessment. On the second page of the “Commander’s Summary,” I underlined a passage I had not anticipated finding: “Failure to gain the initiative and reverse insurgent momentum in the near-term (next 12 months)—while Afghan security capacity matures—risks an outcome where defeating the insurgency is no longer possible.” In other words, the U.S. could lose the war by September 2010.

A culture of can-do pervades the U.S. military, and generals rarely talk about the “no longer possible,” especially in writing. But this report was sent directly to the secretary of defense. I had to reread the passage, and I put a red check mark by it.

As I continued, it was clear the report was much more than a routine battlefield assessment. There was a desperate urgency to it. This is a cry from the heart, I realized. McChrystal said his forces were “poorly configured” to conduct protect-the-population security.

I underlined, “Pre-occupied with the protection of our own forces, we have operated in a manner that distances us—physically and psychologically—from the people we seek to protect.” It baldly said that “we run the risk of strategic defeat” because of operations that cause civilian casualties. I circled the notion of “strategic defeat,” which could mean losing the war. “Defeat”? Generals just do not normally talk this way.

Then on the fourth page of the report’s summary, my red pen darted under a sentence that blew the whistle on McChrystal’s own command: “Almost every aspect of our collective effort and associated resourcing has lagged a growing insurgency—historically a recipe for failure” in counterinsurgency. There was that word again, “failure.” I then read that the Afghan security force “will not have enough capability in the near-term given the insurgency’s growth rate,” so he proposed a “bridge capability” of more coalition troops.

Next, the pen went under, “The status quo will lead to failure …” I got the message, and I wondered how this assessment had gone over with Gates, who, after all, had been secretary of defense for the last 20 months—secretary of defense in a losing war, according to Gates’s own new commander on the ground.

Gates had told the president back during the first months of the administration, after the president had authorized 21,000 more troops, that he hoped there would be no more troop requests.

Although McChrystal’s assessment did not include a troop request, there was definitely going to be a large one. Other sources were telling me it would be 40,000 or more, as a middle option.

“We cannot succeed simply by trying harder,” I read. “The entire culture—how ISAF [International Security Assistance Force] understands the environment and defined the fight, how it interacts with the Afghan people and government, and how it operates both on the ground and within the coalition—must change profoundly.” Commanders rarely report on the need for “change.” Instead, they order it.

McChrystal said that accomplishing his mission required “defeating the insurgency, which this paper defines as a condition where the insurgency no longer threatens the viability of the state.” He used some form of the word “defeat” 14 times.

I underscored this sentence: “The weakness of state institutions, malign actions of power brokers, widespread corruption and abuse of power by various officials, and ISAF’s own errors, have given Afghans little reason to support their government.”

Insurgents had “a Taliban ‘shadow government’ that actively seeks to control the population and displace the national government and traditional power structures.” This was new to me and it indicated that the insurgents had penetrated deeper into the various provinces than I had imagined.

Because of “inadequate intelligence,” McChrystal could not say precisely how much of Afghanistan, beyond a “significant portion,” was controlled or contested by insurgents. That was a startling indictment of the intelligence shortcomings.

The report went on to describe the three major Taliban insurgent groups that loosely coordinated with each other: the Quetta Shura Taliban, the Haqqani network, and Hezb-e-Islami Gulbuddin. The Quetta Shura Taliban had established an alternative government in direct competition to Karzai’s authority. “They appoint shadow governors for most provinces, review their performance, and replace them periodically,” the report said. “They install ‘shari’a’ [Islamic law] courts to deliver swift and enforced justice in contested and controlled areas. They levy taxes and conscript fighters and laborers.”

McChrystal laid out his initial plans for an ISAF future offensive, saying that coalition forces would “focus on critical high-population areas that are contested or controlled by insurgents, not because the enemy is present, but because it is here that the population is threatened by the insurgency.” He then divided the Afghan provinces into three groups based on the extent of insurgent presence and listed the order in which he might launch an offensive.

The assessment featured a grim four-page appendix on the Afghan prison system, which had become “a sanctuary and base to conduct lethal operations” against the Afghan government and ISAF troops. “There are more insurgents per square foot in corrections facilities than anywhere else in Afghanistan,” it said.

Near the end, I read the general’s overall conclusion: “Failure to provide adequate resources also risks a longer conflict, greater casualties, higher overall costs, and ultimately, a critical loss of political support. Any of these risks, in turn, are likely to result in mission failure.”

By the time I had finished reading, there was little doubt in my mind that the report should be published immediately.

That same Friday night, I e-mailed Marcus Brauchli, who had been executive editor of The Washington Post for slightly more than a year, to let him know I had the report and thought he ought to read it. We met at the Post the next morning, Saturday. Brauchli read the report quickly and said he thought it should be published at once and in full.

I called my source and asked that the ground rules be changed.

“When my book comes out next year,” I said, “this assessment will be such old news, it will not be news at all. It will be irrelevant.” It is news now, I said.

After a few questions, my source agreed and I promised to not identify that person in any way.

Brauchli asked me to call both the White House and the Pentagon to explain that we had a full copy and planned to publish it in the next day or two but wanted them to address which parts, if any, should not be made public and for what reasons.

The June 30, 1971, Supreme Court decision on the Pentagon Papers case, nearly four decades earlier and just three months before I joined the Post, opened the door for such conversations with the government. In its 6 to 3 ruling, the court essentially said the government could not restrain the press before publication of classified documents, which permitted The New York Times and The Washington Post to continue publishing the top secret 47-volume Vietnam War study, which showed that the government had repeatedly lied to the public about the war.

Because the government could not legally stop us from publishing the McChrystal assessment, we had the upper hand in listening to arguments for deleting passages from the report. For the Pentagon Papers, the Times and Post did not consult the government in advance. To do so would have alerted the government and likely resulted in a court action to stop publication, which is exactly what the government did in federal court after the initial articles ran. The beauty of the Supreme Court’s Pentagon Papers ruling—which forbids prior restraint—is that it encourages us to ask the government for their specific objections to the publication of classified documents.

I reached General Jones by phone on Saturday. He was on his boat in the Chesapeake Bay. I explained that I had the full 66-page McChrystal assessment and planned to publish it but wanted to hear from him and the Pentagon first.

“It will make the president’s job more difficult,” he said. Publication would give “insight to those who are working against us,” meaning the Taliban insurgents in Afghanistan.

I said I thought it sounded a dramatic alarm from the new commander about the course of the war, and the public ought to be informed. We would not publish the page outlining future operations. We wanted to hear arguments if there were other parts we should consider deleting on national security grounds.

“I’m not thrilled,” Jones said. “It is classified.” He also noted that he had lots of questions about the report. McChrystal was “a young four-star,” Jones said. “He is naive.”

I said that on a careful read and reread, I did not see the harm, but we were willing—even eager—to listen to their arguments.

“I have some calls to make,” Jones said.

I called Morrell, the Pentagon spokesman, who said, “They want to fight this,” and that we should expect to hear from someone soon.

Within an hour, about 2 P.M. on Saturday, Gates, Jones, Donilon, and General Cartwright, the vice chairman of the JCS, were on the phone in a conference call to Post editor Brauchli, a Post lawyer and myself.

Gates, who was out of town, said he was asking us to hold off on any article or publication of the assessment for 24 hours. Publication, he said, would be “quite damaging to our efforts in Afghanistan and put the lives of our soldiers at risk.”

General Cartwright added that the report was “an operational and tactical assessment” and publication would allow “the enemy to see where we were going.” He asked me for time to review.

We repeated what I had told Jones about not publishing the page that contained future operations.

Donilon said, “I have not heard an answer to the secretary’s request”—that we wait 24 hours.

Brauchli and I both said it seemed reasonable, and Brauchli wanted to know when and where we could hear all their objections. He would withhold publication of the story, he said, but he wanted to make sure we could meet with someone who would have authority to speak for not just the Pentagon but the White House and the intelligence agencies.

We had an appointment at the Pentagon the next morning, Sunday, at 11 A.M.

• • •

We realized that we would have to listen carefully but be on the alert, ready to separate real claims of national security from bogus ones. We were concerned that the administration didn’t want this damning report to be published. At a press conference two weeks earlier on September 3, right after Gates received the report, the secretary had said, “I don’t believe that the war is slipping through the administration’s fingers.” The McChrystal assessment contradicted that.

In addition, Obama was appearing on five television talk shows that morning to make a plea for his health care reform. Obviously the White House would not want other news stepping on its message.

On Sunday, Brauchli, Rajiv Chandrasekaran, a senior Post reporter who covers the war, and I drove to the Pentagon for the 11 A.M. meeting. Because Gates was away, the representatives from the Pentagon were Cartwright, Morrell and undersecretary of defense for policy Michèle Flournoy. We sat around the conference table in Cartwright’s office.

Cartwright, outgoing and exceptionally personable, said there were three major objections—disclosing future operations, intelligence gaps and anything that might compromise McChrystal’s ability to work with the Afghanistan government or other international partners.

At the beginning of the discussion, it seemed it was a contest among several on the government side to see who could get Brauchli to agree to redact the most. In all, they raised 14 specific concerns. The first real issue was whether to quote McChrystal saying that he needed more forces in the next 12 months or the war “will likely end in failure.” It was his strongest statement. Flournoy argued that publication of the 12-month time frame would allow “the enemy, basically, to kind of hold out” and “redouble” its efforts for just 12 months because it would be taken as an indication that American resolve was limited. She also said that publication of the 12-month limit “if read by the Taliban, could lead to a change of tactics on their part that directly translates into more U.S casualties.”

It was a very direct warning.

McChrystal and his team, she said, had been consulted and “They did not want the time frame in there.”

I argued that it was McChrystal’s core argument and we needed to reflect that.

Brauchli noted that Gates and others had said the United States had about 12 to 18 months to shift the momentum in the war, so McChrystal’s use of 12 months was hardly surprising.

Eventually Cartwright agreed and withdrew their objections, but he wanted the last three words redacted from this sentence: “The insurgents control or contest a significant portion of the country, although it is difficult to assess precisely how much due to lack of ISAF presence AND INADEQUATE INTELLIGENCE.”

To let the Taliban know we had “inadequate intelligence” would only encourage them and allow them freer movement because of the inadequacy.

Brauchli agreed, saying, “I think on the issues of disclosure of intelligence gaps, I think we’ll look favorably on that because I don’t think we need to be pointing that out.”

The three words were removed.

I thought this was reasonable, but I chose to publish them in this book because the gaps became increasingly obvious. Overall, Brauchli and Cartwright agreed to redact the details of future ops and the three words on the intelligence gap.

We were able to publish about 97 percent of the assessment without any objections from the government, and deliver the conclusions and details in the story. That evening, the Pentagon provided us with a declassified version of the assessment with the agreed-upon redactions.

We returned to the Post to edit my draft article for Monday’s edition. The headline in the September 21 Washington Post the next morning stretched across the top three quarters of the front page: “McChrystal: More Forces or ‘Mission Failure.’” The declassified version of the assessment was available on the Post Web site. Within a few minutes, The New York Times all but copied the story almost paragraph for paragraph.

The Internet lit up with reactions. Retired Army Colonel Pat Lang wrote on his blog, “This highly classified document was artfully leaked by those who wish to ‘bulldoze’ Obama and Gates into accepting an unlimited commitment to a nation building counterinsurgency strategy in Afghanistan.”

Peter Feaver, who had been on George W. Bush’s NSC staff, wrote on a blog for Foreign Policy magazine, “The domestic political-military stakes have been ramped up considerably with this leak. It is not quite a 3-A.M.-phone-call crisis, but it is probably the most serious national security test the Obama team has confronted thus far.”

At the morning press briefing aboard Air Force One en route to Troy, New York, Gibbs emphasized to reporters that McChrystal had yet to ask for a specific number of additional troops.

“We’re going to conduct that strategic assessment and do that in a way that lays out the best path forward before we make resource decisions, rather than having this go the other way around where one makes resource decisions and then finds a strategy.”

In my interview with the president nine months later, he said the McChrystal assessment was useful because “it clarified a gap in what had come out of the Riedel report.

“I think the Riedel report retained ambiguity about what our central mission was,” Obama told me. “It was interpreted by some as an argument for a beefed-up force that was conducting a counterterrorism strategy.” With Riedel’s emphasis on Pakistan, some, like the vice president, argued that the strategy should focus on the safe havens in Pakistan being used by al Qaeda and the Taliban insurgents. On the other hand, Obama said, it was interpreted by others as a commitment to a full-blown counterinsurgency strategy “as had been classically laid out by General Petraeus.” But the president said he was not buying into a full counterinsurgency because that meant “what you’re purchasing is responsibility for Afghanistan over the long term.

“And so when the McChrystal assessment comes in,” the president told me, “I think at that point what became clear to me was, we’ve got to get everybody in a room and make sure that everybody is singing from the same hymnal.”