Duncan Boothby, a civilian press official in Afghanistan, resigned in the aftermath of the scandal. McChrystal's top press aide Adm. Greg Smith will be traveling with McChrystal back to Washington, D.C.
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."
McChyrstal said he felt betrayed by U.S. ambassador to Afghanistan Karl Eikenberry for the ambassador's criticism of Afghan president Hamid Karzai in a leaked cable.
Eikenberry would not comment when asked about the story. In a written statement, the U.S. embassy would only say they have seen the article, and that Eikenberry and "McChrystal are both are fully committed to the President's strategy and to working together as one civilian-military team to implement it."
A U.S. embassy spokesperson said McChrystal called Richard Holbrooke, U.S. special envoy to Pakistan and Afghanistan, "to apologize for this story and accept full responsibility for it."
"Ambassador Holbrooke values his close and productive relationship with General McChrystal and the International Security Assistance Force," the statement read.
Hastings' story details the tense relationship between Holbrooke and McChrystal. On a trip to Paris, when McChrystal saw on his Blackberry that he had received an e-mail from Holbrooke, he groaned: "I don't even want to open it."
"The Boss says he's like a wounded animal," an unnamed member of McChrystal's team is quoted as saying.
Democratic Sen. John Kerry, D-Mass., chairman of the Senate Foreign Relations committee who was criticized in the article by one of McChrystal's aides, said today he has "tremendous respect" for McChrystal and that it will be up to President Obama to decide whether the general can continue to serve effectively in his position.
"Everyone needs to take a deep breath and give the President and his national security team the space to decide what is in the best interest of our mission, and to have their face-to-face discussion tomorrow without a premature Washington feeding frenzy," Kerry said in a statement.
An unnamed aide was quoted in the story, saying politicians 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. Frankly, it's not very helpful."
NATO officials were quick with their own response, noting that while "unfortunate," "it is just an article."
"We are in the middle of a very real conflict, and the Secretary General has full confidence in Gen. McChrystal as the NATO commander, and in his strategy," NATO said in a statement.