Can General McChrystal Keep His Job?

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General Stanley McChrystal stands before an Afghan army ceremony on March 25, 2010, in Herat, Afghanistan

General Stanley McChrystal spent more than 30 years in the secretive world of U.S. military special operations, unschooled in the wily ways of Washington. On Tuesday morning he learned that his naiveté could cost him his command of the war in Afghanistan. Cutting comments on the Obama Administration by McChrystal and members of his staff reported by Rolling Stone magazine could not have come at a worse time. Progress in Afghanistan has been slow at best, and criticism is mounting in Congress and elsewhere over the Administration's prosecution of the war.

The magazine's release of the remarks by the general and his aides left Pentagon officials reeling. Many interviewed on background believe McChrystal cannot survive this latest flap — which is not his first. Others, however, say it would be in the Administration's interest to keep the chastened general in charge. His fate is likely to be sealed on Tuesday afternoon, when Defense Secretary Robert Gates meets with President Obama at the White House, as McChrystal flies back to Washington, having been summoned for a meeting on Wednesday. Gates issued a cool statement early Tuesday afternoon, saying McChrystal had made "a significant mistake and exercised poor judgment in this case."

"His opinions should only go through the chain of command," said a retired four-star general, speaking on condition of anonymity. "Once you voice it publicly, you've got to go." A retired admiral disagreed. "I think he'll survive — with one testicle removed," he said. Many expressed surprise that such a story would appear in Rolling Stone. "At least Fallon talked to a war college professor from Esquire," said the admiral, referring to the interview then Admiral William Fallon gave in early 2008 in which he questioned U.S. policy on Iran. He resigned a week later.

With his background in the special ops community, McChrystal has long been seen as a great military officer but one lacking the political polish of his boss, General David Petraeus. "He parachuted into this job without any of the training in dealing with Congress or reporters," said an Army officer who is sympathetic toward McChrystal. "It doesn't excuse it, but it makes it easier to understand."

McChrystal's allies say Gates needs to decide what kind of officer he and Obama want leading this nine-year war. "This is all part of their butch, locker-room, fighting-a-war mentality," an associate says. "Is Gates the new [Donald] Rumsfeld?" — who could tolerate no dissent — "or does he understand that you want aggression and assertiveness in your war fighters?"

Obama and Gates tapped McChrystal for the high-profile role after ousting General David McKiernan last year. "McKiernan was the wrong man fighting the wrong war," the retired general says, comparing McKiernan's traditional Army mind-set to McChrystal's counterinsurgency strategy. "McChrystal is the right man fighting the right war, and they've got a lot invested in him, but I don't think he can survive."

The Rolling Stone article, to be published on Friday, paints a picture of a McChrystal inner circle that seemed caught off guard by the prospect that their words would end up in a magazine. Pentagon officials say McChrystal's staff members feel betrayed by reporter Michael Hastings because they believed the "locker room" comments would not be published. Duncan Boothby, a civilian press adviser to McChrystal, has resigned over the issue. Questions are swirling over the fate of Rear Admiral Greg Smith, the top public-affairs chief in Afghanistan. "One of Smith's key jobs is to protect the general," says a former top Pentagon public-affairs chief.

The article describes McChrystal as "disappointed" by his initial private meeting with Obama last year, and it quotes an aide describing National Security Adviser — and former Marine commandant — James Jones as a "clown." It quotes a McChrystal staffer poking fun at Vice President Biden: "Biden?" the aide is quoted as saying. "Did you say: Bite me?" McChrystal himself is quoted as saying he felt "betrayed" by the leak last year of a classified cable from U.S. ambassador to Afghanistan Karl Eikenberry, who raised concerns over the surge of 30,000 U.S. troops to Afghanistan, now under way.

McChrystal issued a statement on Monday night expressing his "sincerest apology" for the article but did not claim that he or his team was misquoted. "I have enormous respect and admiration for President Obama and his national security team, and for the civilian leaders and troops fighting this war, and I remain committed to ensuring its successful outcome."

McChrystal has been down this path before. Last fall, he drew fire for a speech in London in which he played down a war strategy favored by Biden that relied more on drone strikes than ground-based troops. Following those remarks, Obama summoned McChrystal for a 25-min. dressing-down aboard Air Force One in Copenhagen.

Afterward, Gates said, "It is imperative that all of us taking part in these deliberations, civilians and military alike, provide our best advice to the President, candidly but privately." In war fighting, unlike in baseball, there's a good chance that with two strikes, you're out.