All along there were two US wars in Iraq. There was the public war, in which the Pentagon tried to manipulate the mainstream media into being a “message amplifier,” while some intrepid reporters and bloggers fought back. Then there was the secret war carried out by the Special Operations forces, whose existence was denied even by the Pentagon.

Now the secret operations threaten to completely compromise what remains of the public war in Afghanistan and Pakistan with the ascension of Gen. Stanley McChrystal to top commander from his classified role in running Special Ops in Iraq for five years.

When questioned by the media or senators presiding at his confirmation hearing in a few weeks, Gen. McChrystal may have a simple answer to anything troubling: sorry, that is classified.

The mystique of secrecy may come to shroud all public inquiry about Afghanistan and Pakistan. There are questions to be answered, however.

One is framed on page 380 of Bob Woodward’s book The War Within, in which the author describes a top-secret operation in 2006 that targeted and killed insurgents with such effectiveness that it gave “orgasms” to Derek Harvey, a top aide to Gen. David Petraeus and longtime tracker of Iraqi dissidents. The secret program was led by McChrystal, then a lieutenant general, using signals intercepts, informants and other tools of what McChrystal calls “collaborative warfare” through Special Access Programs (SAPS) and Special Compartmented Information (SCI.) McChrystal, according to the New York Times, conducted and commanded most of his secret missions at night. These missions were consistent with the proposals of Petraeus’s top counterinsurgency adviser at the time, David Kilcullen, to revive the discredited Phoenix Program used in South Vietnam.

This expanding secret war is crucial to understand for three reasons. First, according to Woodward’s claim, it was “more important than the surge” in reducing insurgent violence in Iraq. Second, the Special Ops units served as judge, jury and executioner in hundreds of extrajudicial killings. The targeted victims were from broad categories such as “the Sunni insurgency” and “renegade Shiite militias” or other “extremists.” Third, and most important, the operation was kept secret from the American public, media and perhaps even the US Congress.

Woodward himself agreed to self-censorship, choosing to accept the Pentagon’s argument that to disclose any details “might lead to unraveling of state secrets that have been so beneficial in Iraq.”

And there the matter has been left, without a single follow-up story, investigation or Congressional inquiry.

Three years later, Iraq is far from being a pacified US ally, raising the question of whether the secret killing campaign was partly a desperate effort to get through the 2007-2008 political cycle in the United States.

The prospect of contending with secret counterinsurgency programs is not a secret but a well-known challenge to those on the receiving end in Iraq, Afghanistan and Pakistan. The real point is that Special Operations allows the Pentagon to pull the wool over the eyes of the American public, media and Congress. Nothing requires an explanation, including the actual causes of American deaths.

If that seems a harsh conclusion, consider the one public “blot” we already know about concerning Gen. McChrystal’s war record. An investigation by the Pentagon itself found him guilty of fabricating false information in the drama surrounding 2004 death of Army Ranger Pat Tillman, an Arizona Cardinals football player who was killed by friendly fire in Afghanistan. In 2007, McChrystal was held accountable for a Pentagon cover story that Tillman died from “devastating enemy fire,” when in fact he was killed by accidental rounds from his own unit.

What kind of military leader would falsify the details of a soldier’s death in order to create a patriotic legend for public consumption?

His rise can only mean an intensified campaign of secret–and dirty–warfare in the remote villages of Pakistan and Afghanistan.

The public, the media and the Congress are entitled to know whether and how Gen. McChrystal will become transparent, accessible and accountable as he steps out of the shadows, or whether he will be committing America’s future to the night.