On Monday afternoon, Defense Secretary Robert Gates announced that Defense Secretary Robert Gates Army General asked the top American commander in Afghanistan, David McKiernan, for his resignation less than one year into the job, citing a need for “new thinking and new approaches from our military leaders.” Secretary Gates has appointed Lieutenant General Stanley McChrystal to command US and NATO troops in Afghanistan and supply this “new thinking.”

As much of the coverage noted yesterday morning, it’s exceedingly rare to replace a four-star commander in a war zone—it hasn’t happened since Truman recalled MacArthur during the Korean War. When Army General George Casey’s strategy was tried and found wanting in Iraq, Bush let him finish his term in the theater before kicking him upstairs to the post of Army chief of staff.

But it’s thought that McChrystal will bring a unique approach to the ever-knottier war in Afghanistan, based on his background in unconventional warfare. Unlike McKiernan, who spent most of his career commanding conventional forces, McChrystal has a background in Special Operations—those badass commandos with “direct action” missions like shooting pirates. From 2003 to 2008, McChrystal led the Joint Special Operations Command, or JSOC—whose actual function is shadowy but which is thought to be the command overseeing U.S. counterterrorism missions. Little else is known about it—by Congress or the media—except occasional hints that surface in dispatches from people like Bob Woodward and Seymour Hersh.

Woodward has in fact reported that the expansion of “top-secret” operations in Iraq, ostensibly under JSOC, is the untold true story of recent security gains there, often simplistically attributed to “the surge” alone. And it was during McChrystal’s tenure at JSOC’s helm that an Army combat team, aided by a Special Operations task force, captured Saddam Hussein. McChrystal himself, President Bush accidentally revealed, commanded the team that killed Abu Mousab al-Zarqawi, leader of Al Qaeda in Iraq. (“JSOC is awesome,” Bush later elaborated.)

JSOC has considerably more success fending off the press than, say, the NSA. But in March, it made another of its rare appearances in the news. First, The New York Times reported that the U.S. had, in February, temporarily halted some of JSOC’s raids in Afghanistan, “reflecting a growing concern that civilian deaths caused by American firepower are jeopardizing broader goals there.”

Seymour Hersh was giving a talk at the University of Minnesota around the same time and, citing reporting from a book he’s working on, described JSOC thus:

It’s an executive assassination ring, essentially, and it’s been going on and on and on… Under President Bush’s authority, they’ve been going into countries, not talking to the ambassador or the CIA station chief, and finding people on a list and executing them and leaving. That’s been going on, in the name of all of us.

Hersh later had to backpedal. (“I must drive my editors crazy when I say things that are loaded,” he said.) But he stuck to his guns, so to speak. “JSOC… has been given executive authority by the president in as many as 12 countries to go in and kill, we’re talking about high value targets” without congressional oversight, he told Wolf Blitzer, who rejoined, “Is there anything wrong with that?”

Hersh thinks so. But counterinsurgency scholar Andrew Exum of the blog Abu Muquwama was dismissive.

It’s not like JSOC is some partisan task force that went away when Obama got elected… I don’t think any of us would dispute the need for highly-trained, highly-specialized commandos capable of carrying out ‘capture or kill’ or hostage-rescue missions of some high degree of strategic importance.

In any case, as Marc Ambinder notes, JSOC might now have its day in the Congressional sun. McChrystal must be confirmed by the Senate, and some senators are curious about JSOC. But Ambinder isn’t hopeful that the Senate will render Hersh’s book deal irrelevant.

Knowing how savvy the Defense Secretary is, it’s hard to imagine that McChrystal would have gotten the appointment if he’d been mixed up in potential misconduct or extra-legal behavior that Congress could uncover. The only public blight on McChrystal’s record is his role in the cover-up of Army Ranger Pat Tillman’s death. Congress will be interested to hear him speak about this — it’s hard to get the JSOC commander to testify in public, which was why McChrystal has not spoken about the affair in public — but his confirmation will probably not be jeopardized by this incident alone.

Regardless, JSOC is poised for a return to the news cycle. To the chagrin of New Yorker editors everywhere, that means Hersh is, too.

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Kathy Gilsinan is the associate editor at World Politics Review