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Look through the history of this country and you find a constant theme that goes right back to the earliest days. It's the struggle to balance the relationship between the military and civilian leaders. The troops must fight a war but it's considered essential that civilians always remain in charge.

That broad theme lay behind the strange events of this week when General Stanley McChrystal lost his job for remarks in a magazine. His replacement as commander in Afghanistan is General David Petraeus. And that general will face a more subtle challenge. He doesn't just have to get along with his commander-in-chief He has to build practical working relationships with civilians on the ground.

NPR's Rachel Martin reports.

RACHEL MARTIN: Secretary of Defense Robert Gates and Admiral Mike Mullen defended the president's decision to replace General Stanley McChrystal. Sitting next to his civilian boss, the admiral's message yesterday could not have been more clear.

Admiral MIKE MULLEN (Chairman, Joint Chiefs of Staff): Do not have the right, nor should we ever assume the prerogative, to cast doubt upon the ability or mock the motives of our civilian leaders, elected or appointed. I think it is vital for us to remember that if we lose their trust and confidence for any reason, it's time to go.

MARTIN: General McChrystal lost his job because the comments he and his aides made and quoted in the magazine "Rolling Stone" revealed a rift between him and his staff on the one side and the civilian leaders who define the war policy on the other.

One of the people singled out: the American ambassador in Afghanistan, Karl Eikenberry. The tension between McChrystal and the man who was supposed to be his partner was a poorly kept secret. And as General McChrystal became the primary U.S. contact with Afghan President Hamid Karzai, the relationship between the general and the ambassador fractured.

Mr. ZALMAY KHALILZAD (Former U.S. Ambassador, Afghanistan and Iraq): The importance of one mission, one team, cannot be overemphasized in the counterinsurgency operations.

MARTIN: Zalmay Khalilzad served as U.S. ambassador in both Afghanistan and Iraq. He says the partnership between the top diplomat and the top commander is a precondition for success, especially in counterinsurgency war - a strategy where the lines dividing military missions from civilian ones are often blurred. He points to his own experience working alongside military commanders in both war zones.

In Afghanistan, Khalilzad and his counterpart even made sure their offices were next to each other.

Mr. KHALILZAD: We met at least once a day. Sometimes there were obvious tensions, clearly. But I think at the end of the day we recognized that this was more important than any one of us or any one of the institutions.

MARTIN: There is one recent example of a military/civilian relationship that most experts agree was exceptional: General Petraeus and Ambassador Ryan Crocker worked together in Iraq and oversaw the strategy that became known as the surge. In 2008, Secretary Gates called the Petraeus/Crocker team a, quote, "superb model of military/civilian partnership, and one that should be studied and emulated for years to come." Or, says Senator John McCain, maybe brought back together for one more tour.

Senator JOHN MCCAIN (Republican, Arizona): We might suggest that the consideration be given to reuniting the Crocker/Petraeus team.

MARTIN: That may be wishful thinking by Senator McCain, since Crocker is retired from the foreign service. Still, McCain and others on Capitol Hill say while General McChrystal had to go, more change is needed.

Sen. MCCAIN: We still have concerns about the civilian side of it, and the non-military side of this equation, relations between the ambassador and President Karzai, whether there is sufficient civilian side of this equation on the ground.

MARTIN: Ambassador Khalilzad agrees.

Mr. KHALILZAD: This is an opportunity to see if a team that is functional can be put together with existing people, with General Petraeus in the lead. If not, what other changes need to be made, because a lot needs to happen in a short time, given that - the timeline of July of next year.

MARTIN: That's when President Obama has said he wants to begin withdrawing some U.S. troops from Afghanistan. Doing so could depend on whether the new military command in Afghanistan and the American diplomats there can make peace with each other and take the fight to the enemy.

Rachel Martin, NPR News, Washington.

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