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It had been a rough 16 months for Dennis Blair. The DNI had failed in his effort to name the chief intelligence officer in each foreign capital. The CIA had won and the feud had gone public. Blair had also conducted a nonpublic war against two other sources of power for the CIA. In his view, the CIA was using the President’s Daily Brief as a house rag for telling Obama their triumphs—even something as minor as an operation involving three guys and a pickup truck. He edited out these advertisements for the CIA’s wares, saying, “I’m not going to give that to the president.”

He also went after the CIA covert action programs, attempting to trim them and align them more with overt U.S. policies. “Covert action programs should continually be considered for transition to non-covert activities,” he wrote in one SECRET proposal rejected by the White House.

Blair grew so frustrated that at one point he declared, “I think the CIA is fundamentally an organization that’s like a really finely trained, not very smart, dangerous animal that needs to be controlled very closely by adults.”

By May 2010, President Obama was telling Jones and others, “Isn’t it about time to get rid of Blair?” There had been too many fights with the CIA. And Blair had also pushed too hard for a no-spying agreement with the French that Obama and the rest of the cabinet opposed.

Without informing Blair, members of Obama’s staff began shopping around the DNI job, talking about it with deputy secretary of state Jim Steinberg, Chuck Hagel, a former Republican senator from Nebraska, and John McLaughlin, a former deputy director of the CIA. When word about this reached Blair, he complained and soon had a meeting with Obama.

The president listed his reasons why the retired admiral was not working out as DNI. Blair responded to them in writing, defending himself and detailing his accomplishments.

After reading Blair’s response, Obama phoned him on Thursday, May 20. “I have decided and I’m going to make the change,” the president said.

He then offered Blair a face-saving exit. Take your time, weeks, even months, Obama said. Come up with a personal reason or any explanation. He would support any story Blair wanted, the president said. A smooth transition was in everyone’s interest. After all, they were at war.

Blair was deeply offended. He wasn’t ill. His family was fine. And he had told people he would stay as DNI for four years because part of the problem with the office had been the constant turnover at the top.

“You want me to lie?” Blair asked.

No, Obama said, I didn’t mean that at all.

Fire me, Blair basically said.

That’s exactly what Obama did.

Within several minutes of the conversation, Jake Tapper of ABC News reported on the network’s Web site that Blair was leaving.

About 5 P.M. on June 21, Gates called Jones. “There’s an article coming out in Rolling Stone magazine that’s not very good about McChrystal,” he said. It contained some disparaging and mocking comments from McChrystal and his senior staff about administration officials. One unnamed McChrystal aide called Jones a “clown” who is “stuck in 1985.” McChrystal himself was quoted saying that Obama’s strategy review was “painful” and “I was selling an unsellable position.” Recounting McChrystal’s stay in Paris, including a heavy-drinking evening with his wife and senior staff, the article revealed the commanding general as anti-French. Gates said he planned to release a statement reprimanding McChrystal, but hoped to salvage the situation and avoid a setback to the war strategy.

“I’m not sure that goes far enough,” Jones said. “This is pretty sensational stuff.” The article also quoted unnamed McChrystal aides who took shots at Biden, Holbrooke and Eikenberry.

McChrystal called Biden about the profile. “I have compromised the mission,” he said.

He also apologized to Holbrooke and said he had offered his resignation to Gates.

Later that evening the president met with Emanuel and Jones, who recommended that Obama order McChrystal back to Washington. Don’t do anything now, Jones suggested, but sleep on it.

Obama agreed and the next morning McChrystal was ordered to return to Washington—a dramatic statement in itself. Jones told Gates that protecting McChrystal was noble. “But you don’t want to put yourself between him and the president.”

Gates proposed that he issue the first two paragraphs of his statement criticizing McChrystal, and Jones agreed. “I believe that General McCrystal made a significant mistake and exercised poor judgment,” Gates said in his statement.

At the Pentagon, Geoff Morrell, Gates’s spokesman and confidant, was in agony. It was like seeing a funnel cloud rising for Gates and the whole military establishment. The article would once again expose the messiness and mistrust between the White House and the military. Morrell’s job was to quell what he called the “family feud,” downplay its significance, respond to protect the military without appearing disloyal to the administration. To get into detail about the rift would only further reveal the divide that he believed was, in part, a consequence of the prolonged AfPak strategy review. The fact was that the White House had its version, claiming that the president had dramatically asserted civilian control while the military version was that it had basically gotten what it wanted. The tensions had abated in public and since gone underground. Now they were headed for another public airing. He tuned into Gibbs’s noon press briefing, knowing that the press secretary would be operating under presidential instructions.

“Is removing the general from his position at least an option the president is considering?” one reporter asked.

“I would say all options are on the table,” Gibbs replied.

Fair enough, Morrell thought.

“I think the magnitude and graveness of the mistake here are profound,” Gibbs said next, shooting way beyond Gates’s comment that it was a mistake and poor judgment.

Gibbs reported that Obama was “angry” upon seeing the article and was recalling McChrystal “to see what in the world he was thinking.”

“So you’re questioning whether or not General McChrystal is capable and mature enough for this job he has?”

“You had my quote right,” Gibbs said.

Morrell was sickened. Gibbs was relishing it too much, “like a pig in shit,” as he told others later.

The next day Obama accepted McChrystal’s resignation, and he proposed that Petraeus take over. Though it would involve a technical demotion because as central commander Petraeus was the boss, it was an idea that would address both the military and political problems. The Iraq hero would come to the rescue of Afghanistan.

Obama met alone with Petraeus for 40 minutes. Obama told me, “Dave Petraeus was the only person who fit the bill.”

I noted that it was a demotion.

“He certainly doesn’t consider it a demotion,” the president said. “I think that Dave Petraeus understands that this is the single most important job that anybody in our military could be doing right now.”

At 1:43 P.M. on Wednesday, June 23, the president announced the changes in the Rose Garden. He said he admired McChrystal’s “long record of service,”

“remarkable career,” and “his enormous contributions.” Pulling out all the stops, the president added, “Indeed it saddens me to lose the service of a soldier who I’ve come to respect and admire.”

He said that Petraeus would “maintain the momentum and leadership that we need to succeed.

“He is setting an extraordinary example of service and patriotism by assuming this difficult post.” Calling Afghanistan “a very tough fight,” Obama said, “I welcome debate among my team, but I won’t tolerate division.”