The Rolling Stone article described the general's first one-on-one meeting with Obama as awkward, leaving the reader with the impression that the president did not come prepared.
An adviser to McChrystal was quoted calling the meeting a "10-minute photo-op."
The adviser continued: "Obama clearly didn't know anything about him, who he was. Here's the guy who's going to run his f---ing war, but he didn't seem very engaged. The Boss was pretty disappointed."
McChrystal personally commented on the three-month review period last year during which Obama and his advisers charted a new strategy in Afghanistan.
"I found that time painful," McChrystal said. "I was selling an unsellable position."
During the Afghan war strategy review, Vice President Biden was on the other side of the fence from McChrystal, advocating a stripped-down counterterrorism approach while McChrystal pushed for boots on the ground.
The lingering friction was apparent in the article. It depicted McChrystal and his aides imagining how the general would answer press questions about Biden's involvement.
"Are you asking about Vice President Biden? Who's that?" McChrystal said, laughing.
An adviser chimed in: "Biden? Did you say: Bite Me?"
McChrystal's civilian counterpart was singled out for some of the most searing criticism in the piece. U.S. Ambassador to Afghanistan Karl Eikenberry had thrown a wrench into the review process last fall for the Afghanistan war strategy when he sent cables to Washington expressing concern about McChrystal's approach and Afghan President Hamid Karzai's reliability as a U.S. partner.
McChrystal told Rolling Stone he felt "betrayed" by the ambassador and suggested Eikenberry was just trying to look good for posterity.
"I like Karl, I've known him for years, but they'd never said anything like that to us before," he said. "Here's one that covers his flank for the history books. Now if we fail, they can say, 'I told you so.'"
The criticism at National Security Adviser James Jones in the Rolling Stone article was short and not-so-sweet.
An aide was quoted calling the retired four-star general a "clown" who is "stuck in 1985."
The McChrystal team came across as having a complex disdain for veteran diplomat Richard Holbrooke.
One member of the team was quoted saying McChrystal compares Holbrooke to a "wounded animal."
"Holbrooke keeps hearing rumors that he's going to get fired, so that makes him dangerous," the staffer said. "He's a brilliant guy, but he just comes in, pulls on a lever, whatever he can grasp onto."
The article depicted a scene in Paris where McChrystal was checking his BlackBerry.
"Oh, not another e-mail from Holbrooke," the general said. "I don't even want to open it."
After reading the message aloud and putting the BlackBerry away, an aide joked: "Make sure you don't get any of that on your leg."
McChrystal called Sen. John McCain, R-Ariz., and Sen. John Kerry, D-Mass., on Tuesday to discuss the Rolling Stone article, likely because of a line attributed to a member of his staff.
The aide was quoted saying lawmakers like McCain and Kerry "turn up, have a meeting with Karzai, criticize him at the airport press conference, then get back for the Sunday talk shows."
The aide said, "Frankly, it's not very helpful."
It's hardly a rarity these days for an Obama administration official to scold the wayward Afghan president, but the Rolling Stone piece put the McChrystal staff on the record, too.
In the article, a top adviser was quoted saying: "He's been locked up in his palace the past year."
The profile, though, explained how McChrystal has worked hard building Hamid Karzai's public image in Afghanistan and has the "best relationship" with the foreign leader. Karzai expressed his support for McChrystal through a spokesman on Tuesday.
The Rolling Stone article opens by describing how uncomfortable McChrystal was attending a diplomatic dinner in Paris. He and his advisers had no qualms about expressing it.
"I'd rather have my ass kicked by a roomful of people than go out to this dinner," the general said.
An aide who told the reporter that McChrystal was meeting up with "some French minister" also added: "It's f---ing gay."
Rolling Stone's profile on Gen. Stanley McChrystal brought out raw nerves and sore feelings from the top U.S. general in Afghanistan and his closest advisers. On background and on the record, the general and his staff seemed to leave no stone unturned and no official unscathed, including the president himself. Looking for the juicy bits? The following is a guide on everyone who got roasted by team McChrystal -- though with the general being summoned to Washington to explain himself, the ultimate roasting may be reserved for him.