You can read Gen. McChrystal’s apology in full here at the Washington Independent. No “clarification” that I expected last night after seeing the AP writeup of McChrystal’s Rolling Stone interview disrespecting the Obama administration. “It was a mistake reflecting poor judgment and should never have happened,” McChrystal emailed reporters instead. “Throughout my career, I have lived by the principles of personal honor and professional integrity. What is reflected in this article falls far short of that standard.” You think?

McChrystal gets called to the White House on Wednesday to direct the monthly Afghanistan/Pakistan briefing — oh, and to explain himself and see if he can keep his job. As I wrote for the Washington Independent, firing him carries its risks. There’s only a year to go before the July 2011 date to begin the transition to Afghan security responsibility and the Kandahar tide is starting to rise. It’ll be hard to fire McChrystal without ripping the entire Afghanistan strategy up, and I’ve gotten no indication from the White House that it’s interested in doing that. On the other hand, if senior administration officials are and I just haven’t picked up on it, McChrystal just gave them their biggest opportunity.

And what an opportunity. You can read the Rolling Stone profile through Politico. The amazing thing about it is there’s no complaints from McChrystal or his staff about the administration on any substantive ground. After all, McChrystal and his allies won the argument within the White House. All the criticisms — of Eikenberry, of Jones, of Holbrooke, of Biden — are actually just immature and arrogant snipes at how annoying Team America (what, apparently, McChrystal’s crew calls itself) finds them. This is not mission-first, to say the least.

In fact, you have to go deep in the piece to find soldiers and officers offering actual critiques — and what they offer is criticism of McChrystal for being insufficiently brutal. Everyone of them quoted here is a mini-Ralph Peters, upset because McChrystal won’t let them “get our fucking gun on,” as one puts it. I have a lot of respect for Michael Hastings, the author of the profile, but there are many greyer shades of on-the-ground military perspective than that, and I’ve seen them up close. But Hastings does a good and insightful job of showing that McChrystal is stepping into a diplomatic vacuum and acting as an advocate for Hamid Karzai despite Karzai’s performance in office.

We’ll have to wait for Wednesday to see if McChrystal keeps his command. My guess is he’ll stay, because now the White House knows that a chastened McChrystal isn’t going to say anything else outside of his lane to any reporter. McChrystal’s apology, emailed to me and other reporters well before the Rolling Stone story dropped, suggests that he wasn’t trying to walk away from his command in a blaze of arrogance. But it’s on him to repair his relationship with his colleagues and his bosses.

Update, 8:51 a.m.: You know, all that said — Yesterday, Gates passed over Gen. James Mattis for Marine Corps commandant. If Obama wants to cashier McChrystal but not overhaul the entire strategy, Mattis is an option. Whether he’d do it is another thing, since he’s the outgoing commander of U.S. Joint Forces Command, so taking over ISAF will technically be a step down. But Mattis will otherwise retire from the Marines, so maybe he wouldn’t see it that way.