Mr. Obama said that he will following a one-on-one meeting with the commander before the president's White House review of Afghanistan and Pakistan Wednesday morning.
Calm and introspective in public, if a bit brusque, the lanky four-star general, 55, has never been one to suffer fools gladly. But challenging the president and his team is another matter, so he was summoned to the Oval Office on Wednesday to explain remarks he made in a magazine interview.
People who know McChrystal say his comments in the Rolling Stone story, which is filled with scorching assessments of the commander's colleagues in the administration, were grave errors in judgment brought on by the stresses of a difficult war and complicated by the general's undisciplined staff.
CBSNews.com Special Report: Afghanistan
But they also note that the ultimate cause of the furor is probably McChrystal's blunt and uncompromising instincts, the very traits that earned him the job.
"They brought somebody in to be a hard-nosed realist," said Anthony Cordesman, a national security analyst with close ties to the Defense Department. "You brought somebody in to get the job done after eight years of neglect and failure. You brought somebody in basically to fight his way through the bureaucratic and organizational barriers."
McChrystal wasn't trained to maneuver inside the Washington political machine. He spent most of his long military career in the dark world of special operations, including five years as head of Joint Special Operations Command at Fort Bragg in North Carolina.
Unlike many successful military officers, McChrystal's resume includes only two years spent at the Pentagon - once as a vice director of operations on the Joint Staff, from 2002 to 2003, and again in 2008 for a brief stint as director of the Joint Staff - before being picked by Obama in May 2009 to run the war.
More on McChrystal's Misstep:
McChrystal Ordered to W.H. to Explain Critique
McChrystal, Staff Disparage Team Obama
McChrystal Apologizes for Critical Remarks
Much of his career has been spent on the front lines in the war on terrorism, studying al Qaeda and orchestrating secret raids. In 2006, his operation was credited with nabbing Abu Musab al-Zarqawi, the leader of al Qaeda in Iraq and one of the most-wanted fugitives.
His special operations forces that year were also accused by human rights activists of abusing detainees at Camp Nama at Baghdad International Airport.
But it wasn't until Mr. Obama chose him as the top commander in Afghanistan that McChrystal was thrust into a public debate. His predecessor, Gen. David McKiernan, had been on the job for less than a year and wanted more troops. But Obama's political base, including most Democrats in Congress, didn't want an escalation of the war.
Defense Secretary Robert Gates said his decision to fire McKiernan and hire McChrystal was not because he disagreed with McKiernan's repeated requests for more forces.
But Gates said he believed the war could not be won by military means alone. So he turned to McChrystal, who as a former Green Beret was intimately familiar with counterinsurgency tactics that, it was hoped, could swing the war around.
By the fall of 2009, McChrystal had decided that more troops were needed and sent the Pentagon a secret request for 40,000 reinforcements.
The request leaked, and White House aides were infuriated. They believed McChrystal had put Mr. Obama in a dilemma - ignore a decorated war general, or send more troops at the expense of political support.
Later that year, Mr. Obama agreed to send 30,000 more troops to Afghanistan on the condition they begin leaving by July 2011.
In the magazine article, McChrystal complained that Obama had handed him "an unsellable position" on the war. "I found that time painful," he said.
Now, says Cordesman, Mr. Obama might have trouble properly filling McChrystal's shoes if he decides to fire him. "You don't have any replacements with the same experience," he says.
McChrystal previously drew criticism for the handling of the friendly fire shooting of Army Ranger Pat Tillman, a former NFL star, in Afghanistan. An investigation at the time found that McChrystal was "accountable for the inaccurate and misleading assertions" contained in papers recommending that Tillman get a Silver Star award.
McChrystal acknowledged he had suspected several days before approving the Silver Star citation that Tillman might have died in friendly fire. He sent a memo to military leaders warning them of that, even as they were approving Tillman's Silver Star. The award's citation claimed Tillman had "put himself in the line of devastating enemy fire."
Still, McChrystal told investigators he believed Tillman deserved the award. In 2007, the Army overruled a Pentagon recommendation that McChrystal be held accountable for his "misleading" actions.