They finally found Zarqawi by following his spiritual adviser to a house where the terrorist leader was staying. McChrystal called in an air strike.
"I had every expectation that his wife and children were there with him," he said.
"Getting him was just worth the price of killing innocents?" Martin asked.
"This was a man who had not only personally been involved in killing, but had literally precipitated thousands and thousands of deaths in Iraq. His cruelty, en masse, was stunning . . . It was so necessary to stop him, I didn't hesitate."
McChrystal spent nearly five years in Iraq working out of a plywood headquarters. His next combat tour was as top commander in Afghanistan.
"You were the 12th American to take command in Afghanistan in, what, eight years? What does that say about the way we were fighting that war?" asked Martin.
"I think it says a lot," McChrystal said. "Because Iraq had been the main effort or the priority for the American military for a number of years. In fact, Afghanistan had been sparely resourced with talent, with numbers, with technology and what-not."
"Except guys are getting killed."
"Well, that's the issue."
He convinced President Obama to send in 30,000 more troops, but as McChrystal writes in his memoir, "My Share of the Task," there was an "unfortunate deficit of trust" between the military and a White House wary of being dragged into a Vietnam-like quagmire.
"This must be a really big deal, not having trust between the commander in the field and the commander in chief," said Martin.
"It's a challenge. While I think the relationships were positive and I think the relationships were professional, they had not yet grown into the kind of trust that allows you to make extraordinarily difficult decisions, often under time pressures."
Then Rolling Stone published "The Runaway General," depicting McChrystal and his closest aides trash-talking their civilian leaders.
"I was awakened about, I think it was two in the morning," McChrystal said, "and I was told there was a problem, that the Rolling Stone article was about to come out and it was bad. . . . I was completely surprised."
McChrystal and his wife Annie had been celebrating their 33rd anniversary while on a trip to Paris to brief French officials on Afghanistan. They had invited the Rolling Stone reporter, Michael Hastings, to join them for late night drinks with McChrystal's staff.
Annie recalled, "That evening when Stan and I were getting ready for bed, I said to him, 'Wow, I am so glad the reporter saw that evening and got to see what I saw, was just this amazing group of men who have been serving together for so many years and in this fight for so many years, and that kind of connection that they all had to each other."
But the anonymous quotes attributed to McChrystal's staff were devastating, including one about a meeting with President Obama: "The boss was pretty disappointed."
"My whole life, I'd expected that I could get killed in war," McChrystal said. "In my wildest dreams I never once thought I could be accused of anything approaching disloyalty or disrespect."
McChrystal was recalled to Washington to meet with the president face-to-face.
"What did you say to your staff?" Martian asked.
"That they didn't fail. You owe that to them."