Gen. Stanley McChrystal (Louie Palu/ZUMApress.com)

By the time you read this, Gen. Stanley McChrystal may very well have lost his command in Afghanistan. McChrystal is headed to a White House Situation Room meeting with President Obama on Wednesday; Time’s Joe Klein reported Tuesday afternoon that the general offered to resign after making disrespectful comments about senior Obama administration officials to Rolling Stone’s Michael Hastings. Whether Obama takes him up on his offer is a different story.

[Security1] And in some ways, it’s a less important decision than another one Obama must make: whether to take the opportunity to change the course of the administration’s strategy in Afghanistan. But if Obama has a chance to use the McChrystal controversy to overhaul his strategy, all signs indicate that he’s not interested.

The past two months in Afghanistan have been brutal. Since returning from a Washington summit with Obama, President Hamid Karzai acrimoniously parted ways with two of his top security officials, men trusted by the U.S. who believe Karzai’s attempts at outreach to the Taliban to bring the war to a close represent capitulation. A United Nations report released this weekend documented a rise in violence in southern Afghanistan ahead of a crucial attempt at pushing the Taliban out of Kandahar, the south’s most populous city. McChrystal had to slow down his push to provide what he calls a “rising tide” of security for Kandahar in order to secure buy-in from residents, as Karzai pledged his support for the operation at a mostly supportive local shura only last Sunday.

What remains unclear from any Kandahar planning is the effect even a successful operation will have on the overall strength of al-Qaeda’s allies in Afghanistan — and al-Qaeda itself, across the border in Pakistan. “There was good reason to drive al-Qaeda out of Afghanistan, but there’s no good reason to stay in the place,” said Douglas Macgregor, a retired Army colonel and a skeptic of counterinsurgency. “I don’t see any evidence [Obama's] suddenly going to summon the wherewithal to change course, but frankly this is an opportunity for him to do precisely that.”

If Robert Gibbs’ press briefing Tuesday was any indication, Macgregor has a point about Obama’s wherewithal. Gibbs, the White House press secretary, couched his and the president’s disapproval of McChrystal’s comments by questioning whether McChrystal was committed to implementing Obama’s strategy. “We’re here to implement a new strategy,” Gibbs said in his Tuesday briefing, and “that’s what we want everybody from the ambassador to the combatant commander to anybody else involved with this to focus on.” Gibbs emphasized that the mission in Afghanistan “is bigger than anybody on the military or the civilian side” — signaling that no officer is irreplaceable — and that it’s incumbent on the administration’s national security team “not to re-litigate” the internal autumn debate over Afghanistan strategy.

It was a surprising remark from Gibbs. McChrystal’s comments to Rolling Stone didn’t express any dissatisfaction with either the strategy or the resources he’s received to implement it. That’s probably because Obama ultimately embraced most of McChrystal’s favored approach: a rededication to counterinsurgency in Afghanistan, backed by an increased complement of 30,000 new troops until July 2011, after which Afghan police and soldiers are to gradually assume primary security responsibilities. In the article, McChrystal merely sniped at his civilian superior, Vice President Joe Biden, who favored a more modest course in Afghanistan, and disrespected two of the senior State Department officials who are key to counterinsurgency in Afghanistan this year, Amb. Karl Eikenberry and Richard Holbrooke, the administration’s special representative for Afghanistan and Pakistan.

But while McChrystal may not have meant to damage the strategy he helped create, the dismissive attitude toward the Obama team that he and his senior aides displayed to Rolling Stone put the president in a corner. “To take McChrystal out now and keep the deadline in place means that everything goes somewhat rudderless while time advances,” said a former senior U.S. diplomat who would not talk for the record because of the sensitivity of Obama’s impending decision. “That would be very deleterious to the policy. But to keep him in place would be harmful to the president’s authority. He has to decide what hit he wants to take.”

An additional factor: The short list for replacing McChrystal is heavy on counterinsurgents, further underscoring Gibbs’ emphasis on fidelity to the current strategy. Army Lt. Gen. David Rodriguez is McChrystal’s deputy, head of the International Security Assistance Force’s Joint Command, responsible for overseeing day-to-day military operations. Marine Gen. James Mattis, the head of U.S. Joint Forces Command, is perhaps the Marines’ leading counterinsurgency advocate. (A spokeswoman for Mattis told The Washington Independent on Tuesday, “General Mattis serves at the pleasure of the President, and is completely focused on his assignment as Commander, U.S. Joint Forces Command.”) Marine Lt. Gen. John O. Allen is the deputy commander of U.S. Central Command, where he serves under the military’s foremost counterinsurgency theorist-practitioner, Gen. David Petraeus. A choice that would indicate Obama intends to shift course would be Navy Adm. Eric Olson, the head of U.S. Special Operations Command, who recently criticized counterinsurgency for an insufficient focus on “countering the insurgents” — that is, battling them instead of securing populations from them — but Olson said at a recent conference that many of his criticisms are issues of degree, rather than wholesale rejection.

If Obama ends up making no changes to his strategy ahead of a scheduled December review and opts to keep his chastened commander, McChrystal will have to repair his relationship with his civilian partners if he’s to have any hope of achieving the unity of effort that counterinsurgency theory considers imperative. “I don’t know if I’d say it’s untenable, but he’s obviously in a difficult position,” said Mark Moyar, the author of a recent book on command in counterinsurgency who will arrive in Afghanistan next month to advise the U.S. military. “Most of [the offensive comments] came from his staff. Perhaps if he changed some members of his staff, it’d be possible to salvage” McChrystal’s command.

Sean McFate, a fellow with the New America Foundation and foreign policy adviser to the Obama campaign who used to work for McChrystal as a young officer with the Army’s 82nd Airborne Division, said the administration’s approach in Afghanistan had yet to resolve a fundamental “disunity” that stretches beyond the personalities at the top of particular civilian and military billets. “The national security establishment has to decide if this is ultimately a civilian mission or a military mission,” McFate said, echoing a discarded proposal last year to appoint an official to oversee the implementation of both civilian and military aspects of the strategy. The Rolling Stone article “points to a fallacy of the ‘whole-of-government’ approach. It’s not clear if it’s civilian or military, and it’s certainly not both.” McFate made it clear that he has not spoken to McChrystal in years.

Officials and analysts cautioned that not all of the 30,000 surge troops have yet arrived in Afghanistan, making firm judgment on the strategy’s prospects ahead of December premature. Administration officials pledged last year that as they implement their strategy, they will take “a hard look at the strategy itself” in a review scheduled for December, as Defense Secretary Robert Gates told Congress. But last week, Petraeus and Undersecretary of Defense Michele Flournoy played down the importance of the review, characterizing it as a more aggressive version of the monthly administration-wide examinations of progress — which McChrystal will attend on Wednesday.

In his only public comments on Tuesday ahead of meeting with McChrystal, Obama said his decision would be “determined entirely on how I can make sure that we have a strategy that justifies the enormous courage and sacrifice that those men and women are making over there, and that ultimately makes this country safer.”

But that only begs the question of whether that’s Obama’s current strategy or some alternative. In Kabul and Islamabad, the former diplomat said, the U.S.’s chosen Afghan and Pakistani partners are looking for guidance as to the meaning of Obama’s July 2011 timeline, regardless of how often administration officials have publicly stated they want “long-term partnerships” with both Afghanistan and Pakistan. “Is it a conditions-based start of a slow process [of withdrawal], as Petraeus and Flournoy said, or is it more [in line with] quotes from Biden and impressions given by the president stressing the deadline” as the beginning of the end of the U.S. military presence in the country, the diplomat asked. “That’s a strategic question, one that only Obama can ultimately provide guidance on.”

Now U.S. strategy toward Afghanistan is comparatively robust — which may be damning with faint praise — and the resources devoted to a war in its ninth year are greater than they’ve ever been. But the focus of that effort is no longer on the east of the country. It’s in the also-Pashtun south, the heartland of the Taliban and the more densely populated region, befitting a strategy that considers popular sentiment to be ultimately decisive.

In the east, troop numbers have grown at a slower pace than in the south, and Gen. Stanley McChrystal has decided to pull back from harder-to-defend areas on the Pakistani border disconnected from significant population centers, as with the U.S. withdrawal from the bloody Korengal Valley earlier this year. Only 4,000 of President Obama’s 30,000 troop increase are devoted to the east.

Whatever the merits of that decision, al-Jazeera has documented insurgent fighters who consider the retrenchment to represent their strategic victory. Maj. Gen. Curtis Scaparrotti, the commander in Regional Command-East for the past year, hasn’t claimed major victories over the insurgents. “I think that in terms of strength within RC East, I don’t believe that they’re any stronger now than they were a year ago,” he assessed in his final briefing in command of the area earlier this month, adding that he thought his forces now have “greater initiative” in the 14 provinces he’s been responsible for protecting.

All that has placed a number of burdens on the 30,000 NATO troops in eastern Afghanistan. Yesterday, they got a new commander: Maj. Gen. John Campbell of the 101st Airborne Division. And the message during the change-of-command ceremony from Lt. Gen. David Rodriguez, McChrystal’s deputy, was clear: “Keep protecting and supporting the Afghan people.”

It’s an enormous challenge. There are about 10 million Afghans living in the area that Regional Command-East is responsible for securing. While McChrystal in March restricted the circumstances under which U.S. forces can conduct so-called “night raids” — violent intrusions into Afghan homes hunting for insurgents — a quick tally of many of the highest-profile and most inflammatory night raid show they occurred in the east, including Oct. 16 in Ghazni, circa Dec. 27 in Kunar, Feb. 12 in Paktia, March 21 in Wardak and April 28 and May 14 in Nangarhar. It would appear that these sorts of high-intensity missions have, to put it generously, supplemented any switch to a population-protection mission in the east. They’ve also inflamed and alienated many residents.

Reversing that alienation through demonstrated action to provide local security is Campbell’s task for the next year. One asset he’ll be bringing to bear: His counterinsurgency adviser is Doug Ollivant, a retired Army cavalry officer and former member of the Petraeus brain trust in Iraq. Ollivant knows counterinsurgency, but he doesn’t know Afghanistan yet, and the first principle of counterinsurgency is to collect local knowledge. Campbell and Ollivant have a ton to do in RC-East and not a lot of time to do it.

Research assistance for this post was provided by Rachel Hartman.

Significantly, McChrystal acknowledges that his command is a “tighter team” after his staff changes brought him greater control over the troops he leads — presumably a reference to his chief deputy, Lt. Gen. David Rodriguez, who is working to provide greater coherence to the once-diffuse regional commands across Afghanistan. And, characteristically at this point, McChrystal describes Afghan civilians as “the people that we are here to respect and the people that we are here to protect and the people that we are here to enable.”

Coupled with his early and vigorous words of praise for President Obama — subtle message: let’s end all talk of being a loose-cannon general (even if I personally think that was never warranted) — it’s enough to make you say that McChrystal is fired up and ready to go.

Watch:

But it appears that McChrystal is bracketing a discussion of U.S. combat forces from his report:

McChrystal won’t suggest in his report how many additional U.S. or NATO troops would be needed to train those Afghan forces or to boost the U.S. fighting effort, the official said. Any discussion of U.S. or NATO troops will come in the weeks after McChrystal’s assessment is submitted.

Gates met with McChrystal and his deputy, Gen. David Rodriguez, privately in Belgium on Sunday on the defense secretary’s way back from a trip to the Middle East. He had an audience with the president at the White House yesterday afternoon. Don’t know what they discussed, and I certainly don’t know what they discussed about Afghanistan. Both men have expressed skepticism over bolstering U.S. troops in Afghanistan twice in one year. If they view adding Afghan security forces as an alternative to adding U.S. troops to the war, it’s worth wondering if they think U.S. troops will have to fill in the gap in time it takes to field a larger, competent Afghan force.

Beyond that, it’s unclear what guidelines McChrystal will use to assess the war’s fortunes, the objective conditions of Afghanistan, the relevant variables and the prospects for success. At his confirmation hearing last week, he said that success will ultimately be measured by “the number of Afghans shielded from violence.” But he also embraced “limited but necessary” air strikes, even as new Pentagon investigations uncover preventable errors that contribute to Afghan civilian casualties. Very few commanders would explicitly renounce a legal warfighting option, but questions remain about whether the anger with which Afghans view the result of the air strikes render them counterproductive. How McChrystal will tell the difference? If it’s metrics he’s after, the Center for a New American Security proposed some last week.

At least one change McChrystal has recommended might be on the table this week. During his hearing, he indicated that he would like to give Rodriguez operational responsibility for the regional commands around Afghanistan, freeing him to see the larger picture of the war. But because the Afghanistan war is a NATO fight, such a change will require the sign-off of the NATO countries that contribute troops. Enter Gates, who leaves tomorrow for Maastrict and Brussels for two days of NATO summitting, where he’ll probably take the temperature of the allies for such a command-structure change.

Two great pieces in the Wall Street Journal and the Los Angeles Times report that the Pentagon and Central Command may assign a three-star general underneath the overall commander of the Afghanistan war, Gen. David McKiernan, to coordinate day-to-day operations while McKiernan focuses on the country-wide picture. That’s the way it works in Iraq, where a three-star heads up Multinational Corps-Iraq and reports to Multinational Force-Iraq. Arcane? Sure, but many a military analyst has said over the years that the NATO command structure in Afghanistan is confusing and inefficient. It took until last year for the Defense Department to create U.S. Forces-Afghanistan, a command that integrated the NATO mission with the U.S. mission. (Donald Rumsfeld liked the stovepiping so as not to get the U.S. to perform “peacekeeping” operations. Butterfingers!)

Here’s how an anonymous official explained the thinking to the Times’ Julian Barnes:

“You need a general who is, day-to-day, committed to the fight — an operational commander — and a general who is, day-to-day, committed to the governance,” said a senior Defense official who spoke on condition of anonymity because the proposal is still under discussion.

That’s an interesting way of putting it. Afghanistan is a war zone, sure, but everyone claims to understand that it’s primarily a political conflict. What’s the role of new ambassador Karl Eikenberry — himself a former Afghanistan military commander — if the three-star is going to be focusing on promoting more competent Afghan governance? Coordinating the two efforts is valuable, as governance and security need to be mutually reinforcing. And it looks as if the State Department and USAID and other civilian agencies don’t have the deployable manpower to support the governance requirements the Afghan government has identified. But how to avoid militarizing the governance effort if it falls under USFOR-A?

The Journal’s Peter Spiegel reports that the man for the job is Army Lt. Gen. David Rodriguez. Rodriguez recently commanded forces in eastern Afghanistan, which is going to be a major theater of the war over the next year.