The inappropriate comments by Army Gen. Stanley A. McChrystal and his staff about civilian leaders reflected a widespread frustration with White House infighting over the general's one-year-old war plan.
"I think many analysts would not dispute or say they were surprised at the substance of the comments by the general and his staff," said James Jay Carafano, a military analyst at the Heritage Foundation. "Missing in the whole dust-up is that the significant flaws in the Obama plan — the unrealistic timeline and the fact that the White House gave the commanders less force than they thought was most prudent — are still sitting out there."
Sen. John McCain, top Republican on the Senate Armed Services Committee, backed President Obama's decision last week to accept Gen. McChrystal's resignation over remarks in a recent Rolling Stone magazine article. But the Arizona senator acknowledged the unhappiness of commanders in Afghanistan.
"Yes, there is discontent," Mr. McCain told reporters. "Or let me say, there is a lack of coordination and teamwork between the military and civilian side, both at the embassy and other areas in Afghanistan that needs to be repaired. I think that is very clear. But it was not the role of the military or members of the military to make those comments, except up through the chain of command."
Sen. Joe Lieberman, Connecticut independent, said that after Mr. Obama agreed in December to send more troops to Afghanistan, some of his people still balked.
"I'm afraid that there may be some in the administration who never fully accepted that decision by the president and have continued, through leaks and other means, to suggest a different policy," Mr. Lieberman said.
Mr. Obama himself acknowledged the divisions when he announced Gen. McChrystal's resignation.
"I've just told my national security team that now is the time for all of us to come together," he said. "Doing so is not an option, but an obligation. I welcome debate among my team, but I won't tolerate division."
Relations between the White House and Gen. McChrystal soured quickly after the general took command in Afghanistan a year ago.
Ordered by Defense Secretary Robert M. Gates to do a review, Gen. McChrystal submitted a brand new war plan with a request for 40,000 more troops last fall.
Having already sent 21,000 new troops to Afghanistan, Mr. Obama was cool toward another escalation and spent three months deciding. His national security adviser, James L. Jones, a retired Marine general, called the troop request Gen. McChrystal's "opinion." Vice President Joseph R. Biden Jr. lobbied for going in another direction — pulling troops out — as he did in the Senate when President Bush proposed the Iraq surge. The U.S. ambassador in Afghanistan, Karl W. Eikenberry, also advised Mr. Obama in a cable against sending more personnel.
In dueling leaks, both Gen. McChrystal's dire assessment and Mr. Eikenberry's opposition cable found their way into the news media.
Each of those men — Messrs. Obama, Biden, Eikenberry and Jones — came in for derisive remarks by Gen. McChrystal and his aides in the Rolling Stone article.
Mr. Obama eventually provided 30,000 troops, 10,000 less than requested, but he also set a July 2011 date for the start of withdrawal.
Army Gen. David H. Petraeus, tapped to replace Gen. McChrystal, went to great lengths in recent weeks to stress that the date is not the beginning of an exodus, but the beginning of an assessment of battlefield conditions. Yet White House officials fired back that they expect significant withdrawals, sending an unclear message to the Afghans at a time when the U.S. is trying to pull their loyalties away from the Taliban insurgency.
Despite the squabbling, analysts agree, as did Gen. McChrystal, that he committed a major blunder in opening up to a reporter.
"I am of two minds," said Michael O'Hanlon, a military analyst at the Brookings Institution. "Last fall, Gen. McChrystal took too much of the brunt of criticism for poor communications between the White House and the military that were not primarily McChrystal's fault. So I am very sympathetic to him through that whole period."
But Mr. O'Hanlon said that, after effectively winning the policy debate, the general and his staff needed to be "good winners and be charitable and collegial."
"At least for the purposes of the magazine article, they failed to do so," he said. "That is a shame, because McChrystal in particular is one of the most collegial, deferential and team-oriented generals I've known, and I think he was doing a great job in Afghanistan. Unfortunately, they made some major mistakes vis-a-vis Washington at a time when it's particularly perplexing to understand why or how that was necessary."
There was not much sympathy for Gen. McChrystal in the special-operations community, where he, as an Army Ranger, spent years in so-called "black operations." His resume included running the supersecret Joint Special Operations Command, which he led in Iraq to hunt down al Qaeda terrorists.
Some in the field said they hope Gen. Petraeus' first step is to loosen the rules of engagement implemented by Gen. McChrystal, which limited air strikes, night operations and the destruction of terrorist safe havens. Gen. Petraeus may signal his intentions during confirmation hearings Tuesday before the Senate Armed Services Committee. He appeared before the committee earlier this month to discuss Afghanistan.
"We get feedback periodically that troopers feel that they are being held back," he testified. "We don't want that to be the case. That is not the intent. The intent is very clearly just to reduce to an absolute minimum the loss of innocent civilian life, which in a counterinsurgency operation in particular can unhinge you."
Gen. Petraeus, as head of U.S. Central Command, approved Gen. McChrystal's war plan and troop number and generally gave him wide latitude to run operations the way he saw fit. That does not mean Gen. Petraeus, who ran what is considered a successful surge in Iraq, will not change tactics. He will arrive as NATO forces are assembling for major assaults in the Taliban stronghold of southern Afghanistan in late summer or fall, when the surge of 30,000 troops will be complete.
Mr. Gates, who was spared any criticism by Gen. McChrystal in Rolling Stone, appears open to change after Gen. Petraeus is confirmed.
"When he gets on the ground, he will assess the situation for himself," the defense secretary said. "And at some point, he will make recommendations to the president. And that's what any military commander should do. And the president will welcome those recommendations."
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