Funny thing about the new commander of U.S. forces in Afghanistan, Lt. Gen. Stanley McChrystal: for a brief period of time, his name was left out of the Pentagon phone books. That’s because, of course, he was general officer of a series of units whom the Pentagon stubbornly refuses to admit the existence of, even though popular culture and selective leaks have them quite famous and much admired.

Since 9/11, the activities of the Joint Special Operations Command have been hidden, and appropriately so, from the perspective of the government. The Bush Administration declassified the existence of one elite unit, “Grey Fox,” for the benefit of Bob Woodward’s book about the war in Afghanistan. A few commanders of Delta Force, the Army’s top counterterrorist/direct action unit, have written books about the failure to capture Osama Bin Laden. McChrystal and theater commander David Petreaus developed a close friendship over the past several years, and Petraeus came to view McChrystal as a kindred spirit who saw the war and its progression as he did.

An insurgency expert recently retired from the military told me that McChystal shared what Petraeus’s “commander’s intent” the ability to decipher and implement the strategy as the commander in chief intended. The outgoing commander, McKiernan simply did not inspire Petraeus’s confidence.

And here we are. Pentagon officials were reluctant to talk about McChrystal’s most recent position but they did not discourage reporters from assuming that his work in special operations meant that the U.S. strategy will rely quite heavily on the capabilities of special operations forces trained in counterinsurgency techniques.

Andrew Exum, a former Army Ranger who served in Iraq, wrote yesterday on his pseudonymous blog, Abu Muqawama, that “I do know that many policy-makers and journalists think that McChrystal’s work as the head of the super-secret Joint Special Operations Command was the untold success story of the Surge and the greater war on terror campaigns.”

Woodward hinted at some of these missions in his latest book and made a public spectacle out of his refusal to provide details. Basically, these units used sophisticated biometric identification and advances in signal intelligence technology to track hundreds of militants and then killed them. The scope of the Pentagon’s insurgency biometric program is much larger than has been reported; my sense is that hundreds of U.S. intelligence collectors used data collected from secret cameras and scanners set up throughout the high insurgency areas.

Sy Hersh is the Howard Zinn to Woodward’s conventional historian these days, and Hersh is reportedly working a book that would expose a lot about these Pentagon special missions units in the first few years after 9/11. He has reported in the New Yorker that these units were given the authority to track and kill terrorists with minimal oversight, and that special interrogation task forces organized under a program called “Copper Green” were given a green light to use harsh, unapproved interrogation methods against detainees. The Copper Green program might be the Pentagon’s equivalent to the CIA’s “GST” umbrella, the covert series of rendition, collection, and interrogation programs that are being widely debated in Congress right now.

Hersh calls McChrystal the leader of this “executive assassination” unit and promises to reveal more in the future. One can accept the basic truth of Hersh’s allegation that Delta Force and Seal Team Six killed lots of insurgents under a broad classified authority granted to them by the Bush administration without thinking that the actions were somehow wrong or suspect. On the other hand, if the authority was granted illegally if the targets were not terrorists… well, then JSOC will have a problem. We will see.

Even though the activities of the JSOC units are as controversial if not more so than what the CIA or NSA is alleged to have done under the banner of fighting terrorism, there have been few investigations into the conduct, and few calls to investigate. That’s because, in part, Congress doesn’t know a lot about JSOC’s missions and since 2001 has shown them quite a bit of deference. Congressional investigations into detainee policy and Defense Department practices have focused largely on the activities of policymakers and regular units.

McChrystal must be confirmed by the Senate, and some senators have expressed an interest before in learning more about the JSOC’s recent history. 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.