The first Obama administration official to be alerted to the Rolling Stone article that brought down Stanley McChrystal was Vice-President Joe Biden, who was on Air Force 2 when McChrystal called him to apologize. Biden "had no idea what McChrystal was talking about," but back in Washington, press aide Tommy Vietor had already begun printing and handing out copies of the article on paper! because the text in the PDF he received was too small for everyone to read on their beloved BlackBerrys (weren't they all supposed to have iPads by now?), according to Mike Allen's behind-the-scenes blow-by-blow of the White House's response. Obama, Gibbs, and a cadre of national-security aides met late that night, and though recalling McChrystal from Afghanistan to meet with Obama would buy the president some time to make a final decision, it seemed that the general's fate was already sealed, Allen says.
From the moment the president read the article’s opening paragraph (“'How'd I get screwed into going to this dinner?" demands Gen. Stanley McChrystal. It's a Thursday night in mid-April, and the commander of all U.S. and NATO forces in Afghanistan is sitting in a four-star suite at the Hôtel Westminster in Paris”), it was more likely than not that the Afghanistan commander would be sacked. Officials who participated in the discussions say no single passage was fatal to McChrystal. But the opening was really bad: It made the general sound more like a high-school knucklehead than a thoughtful warrior. We’re trying to get more troops from the French, and you’re calling them gay?! (“‘Who's he going to dinner with?’” I ask one of his aides. ‘Some French minister,’ the aide tells me. ‘It's fucking gay.’”) As one aide dryly told Playbook: “The effect on allies was definitely a consideration.”
The Times adds, "It was already clear then...that General McChrystal might not survive." But there was still plenty of discussion, and aides and defense officials spent time playing Devil's advocate to suss out all the pros and cons of dismissing McChrystal. Of all the people most closely involved in the debate, Defense Secretary Robert Gates seems to have expressed the most reservations about changing leadership now, which he believed "would be hugely disruptive." But Obama was "immediately drawn" to Petraeus as a replacement, and thought he "would address Mr. Gates’s concerns."
In their meeting, McChrystal offered his resignation, and Obama accepted. McChrystal "did not lobby for his job." As he told administration officials during his apology calls, the general knew he had "compromised the mission."