By Mark Mazzetti, Julian E. Barnes and Edward T. Pound

Late last August, the Pentagon dispatched Maj. Gen. Geoffrey Miller and a team of some two dozen staffers to Iraq on a mission of the utmost urgency. Months had passed since the United States began its uneasy occupation of Iraq, but a lethal rear-guard insurgency was still claiming the lives of American soldiers almost every day. Saddam Hussein was still on the run, and U.S. commanders had precious little intelligence about who was behind the spate of deadly attacks like the destruction of the United Nations headquarters in Baghdad. Inside the Pentagon, war planners had come to the conclusion that human intelligence was the key to ending the insurgency. And Miller got the task of helping to extract that intelligence from the thousands of prisoners detained inside U.S. military facilities across Iraq.

What Miller discovered when he got there was chaos. Unlike the Pentagon's terrorist detention facility at Guantanamo Bay, Cuba, which Miller had commanded since the fall of 2002, U.S. oversight of the Iraqi prisons was almost nonexistent, and it showed. Exhausted military police were guarding overcrowded cellblocks in the 120-degree summer heat. Morale and discipline within the military police units were at rock bottom. And, most important, there were no established guidelines for interrogating low-level detainees captured during raids in places like Baghdad and Fallujah.

Miller did his homework. Then he submitted his recommendations about how to overhaul the U.S. military prison system. His report went to Lt. Gen. Ricardo Sanchez, the top U.S. military commander in Iraq. These conclusions, largely adopted by Sanchez, led to a dramatic change in how Iraqi prisons were run and how detainees were interrogated. What investigators want to know now is whether these recommendations also set in motion a chain of events that may have led to the abuses at Abu Ghraib prison.

Despite thousands of grisly photographs and hours of congressional testimony, the questions about who should pay for the abuses carried out by the 372nd Military Police Company still far outnumber the answers. Legal procedures have begun for seven low-level soldiers, but what is increasingly clear is that ultimate responsibility doesn't rest solely with a handful of poorly trained troops. The much-awaited testimony of the mild-mannered Maj. Gen. Antonio Taguba last week pointed the finger squarely at the MP s'top commander, Brig. Gen. Janis Karpinski, but there is growing evidence that some degree of culpability may reside further up the chain of command.

The repercussions of the prison scandal are already far more serious than the usual Washington parlor games about who gets to keep his job and who gets the boot. Inside an anonymous room shown on a snippet of grainy video, five hooded men stood above abducted American Nicholas Berg and proclaimed that the abuses at Abu Ghraib "will be redeemed by blood and souls" and that the United States "will see nothing from us except corpse after corpse and casket after casket of those slaughtered in this fashion." Moments later, one of the hooded men shoved the 26-year-old Pennsylvanian to the floor and cut off his head.

That the Abu Ghraib scandal has become propaganda for international terrorists makes U.S. officials all the more determined to publicly punish those responsible for the abuses. This week, Spc. Jeremy Sivits will be the first tried for his alleged offenses, facing a court-martial, open to the press, inside the cavernous Baghdad Convention Center. Sivits is believed to have cut a deal in exchange for a lighter sentence and is likely to testify that soldiers acted without instructions from above. But other accused members of the 372nd MP Company are expected to fall back on a familiar defense, one offered in military trials throughout history: They were only following orders. But orders from whom?

"Influenced." According to Taguba, who last week received star treatment as deferential senators praised his courage for exposing the abuses, the seven MP s may have been "influenced" by the intelligence operatives who controlled detainee interrogations at Abu Ghraib. A separate investigation, conducted by Maj. Gen. George Fay, is examining the role military intelligence soldiers--members of the 205th Military Intelligence Brigade, commanded by Col. Thomas Pappas--may have played in the torture and humiliation memorialized in the photos.

U.S. News has learned that Pappas has already tried to shift blame higher up the chain of command. In a still-classified statement to military investigators, Pappas said changes in interrogation policies were "enacted as the result of a specific visit by Maj. Gen. Geoffrey Miller" to Abu Ghraib last summer. Among those policies were plans to "develop dedicated MP s to support interrogations." The guidelines Miller gave to Sanchez remain classified, but investigators have said they found no evidence that Miller ever advocated the types of abusive behavior that went on in Abu Ghraib. According to Taguba, Miller advised that the MP s be "actively engaged in setting the conditions for successful exploitation of the internees."

Miller's recommendations appear to have formed the basis for a set of interrogation guidelines Sanchez issued in October, guidelines that have become a focus of congressional scrutiny. The guidelines allow sleep deprivation, forcing prisoners into "stress" positions for up to 45 minutes, and threatening them with guard dogs. Late last week, the Pentagon announced it would ban these practices.

Last Wednesday, Defense Secretary Donald Rumsfeld had defended Sanchez's guidelines during congressional testimony, saying that Pentagon lawyers had vetted them before they were implemented. A day later, Rumsfeld's deputy, Paul Wolfowitz, said under questioning from Sen. Jack Reed (news, bio, voting record) of Rhode Island that he was unaware of such a review and conceded that the guidelines may have been in violation of the Geneva Conventions. Says Reed: "All those things raise very serious questions when the rule is no physical or moral coercion." And, according to a former Pentagon official who worked on detainee policy, if the Iraq guidelines been submitted for policy review, they would have raised "red flags." "We would have been concerned over anything that would have been physically coercive," the former official said.

Passed down a confusing command structure without clear lines of authority, the Sanchez guidelines--which condone at least a degree of physical coercion of prisoners--led to the disaster at Abu Ghraib. Ordinarily, the U.S. military relies on a crystal-clear chain of command in which all officers and enlisted soldiers know to whom they answer. Yet the soldiers charged in the Abu Ghraib scandal sat at bottom of a dysfunctional and shifting command structure that even now defies clear explanation.

Contradictions. Two factors in particular confused the question of who was in charge. The first was Miller's visit. Although Miller was outside the chain of command in Iraq, Rumsfeld had blessed his visit, and Miller seemed to exert broad authority over the prison system in Iraq. Second, a November 19 order inspired by Miller's visit put military intelligence in charge of the MP s at Abu Ghraib and directed guards to assist in prisoner interrogations. Last week, Taguba told Congress that this order ran counter to Army doctrine and created confusion. Stephen Cambone, the Pentagon's under secretary for intelligence, who had dispatched Miller to Iraq, disagreed with Taguba, prompting Sen. Edward Kennedy (news, bio, voting record) of Massachusetts to ask pointedly: "If you have two entirely different kinds of viewpoints on this issue, how in the world are the military police . . . going to be able to get it straight?"

In his examination of the 800th MP Brigade and Abu Ghraib, Taguba was sharply critical of Karpinski's leadership. His report says that she failed to ensure that her soldiers understood the protections afforded to prisoners by the Geneva Conventions and that she failed to "enforce basic soldier standards throughout her command." Taguba's assessment of Karpinski appears to rely, in part, on the testimony of Col. Ralph Sabatino, an Army lawyer who worked on detainee issues for the military and the Coalition Provisional Authority. Sabatino, in a sworn deposition obtained by U.S. News, said he often visited military prisons, including Abu Ghraib, and was not impressed with Karpinski's leadership. She has a "mercurial personality" and "tends to fly off thehandle very easily," Sabatino reported, concluding: "She is, I don't think, an effective commander." Sabatino, now a prosecutor for the city of New York, told U.S. News that he could not discuss his evaluation of Karpinski.

Scapegoat? In a series of interviews with U.S. News last week, Karpinski says Sabatino's assessment was severely flawed. She adamantly denied knowing of any serious abuses at Abu Ghraib, said she was a strong leader, and complained that other Army officers were attempting to use her as a scapegoat. She criticized three top generals, including Taguba, saying that he was out to get a third star and was a "kiss-up" to General Sanchez. Karpinski says she won't take the fall for the prisoner abuses and insists--like Colonel Pappas--that Miller's visit to Iraq created the atmosphere that led to the troubles at Abu Ghraib. According to Karpinski, Miller--referring to Guantanamo--said he wanted to "Gitmo-ize" the prison, and during one tense meeting he demanded control of Abu Ghraib in order to make it the focus of interrogation efforts. "You can do this my way, or we can do it the hard way," Miller said, according to Karpinski's account. "General Sanchez said I could have whatever facility I want. I want Abu Ghraib." Miller, who took command of Iraqi prisons last month, has stated that he never urged military police to use harsh methods against prisoners.

Karpinski says she began to lose control of Abu Ghraib soon after Miller's visit, when the 205th Military Intelligence Brigade took over cellblock 1A and eventually 1B, the two cellblocks where the abuses occurred. The transfer of Abu Ghraib was made complete by Sanchez's November 19 order, an order Karpinski says she didn't learn of it until three days later. Last week, Miller reversed the order that put military intelligence in charge of MP s.

Karpinski said she believes Sanchez bears some of the responsibility for the harsh climate inside Abu Ghraib. After a prison riot in November, and a separate incident in which MP s engaged in a shootout with a prisoner, Sanchez, according to Karpinski, demanded that MP s adopt tougher rules of engagement against detainees. "He wanted the [rules] changed to use lethal force first," Karpinski said, and issued an order changing them over her objections. A spokesman for Sanchez for did not respond to written requests for comment on Karpinski's statements.

In her formal rebuttal to Taguba's investigation, Karpinski, a business consultant in civilian life, argues that Taguba did not interview some of her subordinate commanders who could attest to her strong leadership. While she acknowledged some leadership mistakes, she said Taguba's report failed to consider the difficulties of running a prison in the middle of a war zone. Thus far, Karpinski has been admonished for her role in the Abu Ghraib mess, but a more severe punishment could be on its way. Sen. Lindsey Graham, a Republican member of the Armed Services Committee, suggested that the Army consider dereliction-of-duty charges against Karpinski and other officers. "Over time, we will find that this was not just rogue MP behavior," Graham told U.S. News. "How could we let this prison melt down and become the worst excuse for a military organization I've seen in my life?"

Hidden prisons. The controversy ignited by the photos from Abu Ghraib now extends to the archipelago of prisons the United States has packed with suspected jihadists since 9/11. The Pentagon's base at Guantanamo Bay, where some 600 detainees are held, is well known, but there are a half-dozen others, all overseas, including facilities in Jordan, Afghanistan (news - web sites), and the U.S.-British base on Diego Garcia, in the Indian Ocean. U.S. officials have tightly controlled access to these facilities, refusing most requests from even allied governments to interview prisoners. Indonesian security chiefs are furious with Washington, for example, for not allowing them to question Riduan Isamuddin, a senior al Qaeda leader. "They don't want anyone seeing what's happening to these guys," says a counterterrorism official with access to interrogation reports.

The Pentagon's overseers at Guantanamo Bay dispute that, saying that the emphasis during interrogations is on psychological, rather than physical, coercion, along with rewards and incentives. A former government official explains that one common practice is to exploit the phobias of the detainees. For instance, MP s are trained to watch if a prisoner flinches when he hears a dog bark. If that happens, says the official, "You can be sure that there's going to be a dog present during the interrogations."

On his plane to visit Iraq last week, Rumsfeld--with characteristic understatement--said the Abu Ghraib scandal has been "unhelpful" to the U.S. effort in Iraq. Some defense officials say that a more forthright disclosure of the photos could have mitigated the current public-relations disaster. Months ago, some in the Pentagon pressed for release of the photos, but their arguments were rejected. "I think they took a gamble, hoping that the pictures would not get out until after the [June 30] changeover" of sovereignty, says an official who advocated releasing the images. "And they missed it by about eight weeks."

In the wake of Nicholas Berg's murder, even Pentagon officials who had once advocated disclosure of the photos worry that making more images public might further endanger Americans in Iraq. Last week, members of Congress were allowed to view the photos but were admonished by the Pentagon to avoid describing the images in detail. The Pentagon guidelines to lawmakers said that describing the photos would "constitute a violation of the Geneva Convention" that protects prisoners "against insults and public curiosity."