McChrystal got his marching orders as he held a face-to-face meeting at the White House, where he met with the president after a meeting with Defense Secretary Robert Gates at the Pentagon.
The Wednesday meeting preceded a regular session of the administration's strategy team for Afghanistan, held in the White House Situation Room. Normally, McChrystal would have joined via teleconference but he was summoned to Washington as he faced a private flogging over the article that appeared in Rolling Stone.
If not insubordination, the remarks in the Rolling Stone magazine article were at least an indirect challenge to civilian management of the war in Washington by its top military commander.
Military leaders rarely challenge their commander in chief publicly, and when they do, consequences tend to be more severe than a scolding.
"I think it's clear that the article in which he and his team appeared showed a poor -- showed poor judgment," the president said Tuesday, surrounded by members of his Cabinet. "But I also want to make sure that I talk to him directly before I make any final decisions."
Gates hand-picked McChrystal to take over the war last year, calling him a driven visionary with the fortitude and intelligence to turn the war around. Obama fired the previous commander at Gates' recommendation.
In Kabul on Tuesday, McChrystal issued a statement saying: "I extend my sincerest apology for this profile. It was a mistake reflecting poor judgment and should never have happened."
In the Rolling Stone article, McChrystal and his staff described the president as unprepared for their first one-on-one encounter.
McChrystal also said he felt betrayed and blind-sided by his diplomatic partner, Ambassador Karl Eikenberry. Eikenberry remains in his post in Kabul, and although both men publicly say they are friends, their rift is on full display. McChrystal and Eikenberry, himself a retired Army general, stood as far apart as the speakers' platform would allow during a White House news conference last month.
The story characterized the general as unable to convince some of his own soldiers that his strategy can win the nation's longest-running war, and dejected that the president didn't know about his commendable military record.
The article says that although McChrystal voted for Obama, the two failed to connect from the start. Obama called McChrystal on the carpet last fall for speaking too bluntly about his desire for more troops.
"I found that time painful," McChrystal said in the article, on newsstands Friday. "I was selling an unsellable position."It quoted an adviser to McChrystal dismissing the early meeting with Obama as a "10-minute photo-op."
"Obama clearly didn't know anything about him, who he was. The boss was pretty disappointed," the adviser told the magazine.
Some of the strongest criticism was reserved for Richard Holbrooke, Obama's special envoy to Afghanistan and Pakistan.
"The boss says he's like a wounded animal," one of the general's aides was quoted as saying. "Holbrooke keeps hearing rumors that he's going to get fired, so that makes him dangerous."
McChrystal said he felt "betrayed" by Eikenberry for expressing doubts about his proposed troop buildup last year and accused the ambassador of giving himself cover.
"Here's one that covers his flank for the history books," McChrystal told the magazine. "Now, if we fail, they can say 'I told you so."'
Obama agreed to dispatch an additional 30,000 U.S. troops to Afghanistan only after months of study that many in the military found frustrating. The White House's troop commitment was coupled with a pledge to begin bringing troops home in July 2011, in what counterinsurgency strategists advising McChrystal regarded as an arbitrary deadline.
The profile, titled "The Runaway General," emerged from several weeks of interviews and travel with McChrystal's tight circle of aides this spring.
It includes a list of administration figures said to back McChrystal, including Gates and Secretary of State Hillary Rodham Clinton, and puts Vice President Joe Biden at the top of a list of those who don't.
The article claims McChrystal has seized control of the war "by never taking his eye off the real enemy: The wimps in the White House."