Officials feared that McChrystal's influence would be diminished and could jeopardize the momentum of the U.S. counterinsurgency strategy in Afghanistan. At the same time, officials realized how closely tied McChrystal was with the current counterinsurgency strategy, and the fact that Gen. David McKiernan was dismissed from the same job last summer could cause upheaval in operations on the ground.
The government of Afghan President Hamid Karzai threw its support behind McChrystal, portrayed in the article as one of the very few U.S. leaders on the ground who often sided with Karzai.
"The president believes that we are in very sensitive juncture in our partnership, in our war on terror, in the process of bringing peace and stability in Afghanistan," Karzai's spokesman Waheed Omer said in a videoconference. "In that any gap in this process will not be helpful, so we hope that for the sake of the process to move forward smoothly and for the sake of the process not to be interrupted we hope that there is not a change of leadership in the international forces here in Afghanistan."
In the profile by Michael Hastings, published in Rolling Stone, titled "The Runaway General," McChrystal is characterized as an outsider who did not relate well with the administration, and as a military leader who was "disappointed" with his first meeting with the president.
Hastings said McChrystal was fully aware of the notebook and tape recorder that the freelance journalist always had in his interviews.
"It was a sort of natural kind of recklessness that General McCrystal had, that has been with him through his entire career, as I understand it, I hear from the special forces community," Hastings told ABC News' Diane Sawyer Tuesday. "Their willingness to take a risk is a part of their whole persona. And inviting me in, was a obviously a risk, as it always is when you invite a journalist in."
McChrystal and his aides criticized several top U.S. officials, including U.S. special envoy to Pakistan and Afghanistan Richard Holbrooke -- dubbed a "wounded animal." McChyrstal also said he felt betrayed by U.S. ambassador to Afghanistan Karl Eikenberry for the ambassador's criticism of Karzai in a leaked cable.
One of the article's most disparaging remarks comes from an unnamed adviser to McChrystal, who described the general's first meeting with Obama.
"Obama clearly didn't know anything about him, who he was," the aide said. "Here's the guy who's going to run his [expletive] war, but he didn't seem very engaged. The boss was pretty disappointed."
In his apology, McChrystal said he had "enormous respect and admiration for President Obama and his national security team, and for the civilian leaders and troops fighting this war" and said he remains "committed to ensuring its successful outcome."
In the article, McChrystal said the president criticized him for speaking too bluntly about needing more troops last fall.
"I found that time painful," McChrystal said in the article. "I was selling an unsellable position."
The story has raised questions about the issue of trust between the White House and the man running the show in Afghanistan, which has now become the United States' longest war ever.