“I’ll talk to you about discrimination,” he said one morning, while discussing, without bitterness, his early years as an Army officer. “Let’s talk about being refused to be served at a restaurant in public. Let’s talk about having to do things two times, and being accused of not speaking English well, and having to pay myself for my three master’s degrees because the Army didn’t think I was smart enough. So what? Just work your ass off. So what? The hard work paid off.”

Taguba had joined the Army knowing little about his father’s military experience. “He saw the ravages and brutality of war, but he wasn’t about to brag about his exploits,” Taguba said. “He didn’t say anything until 1997, and it took me two years to rebuild his records and show that he was authorized for an award.” On Tomas’s eightieth birthday, he was awarded the Bronze Star and a prisoner-of-war medal in a ceremony at Schofield Barracks, in Hawaii. “My father never laughed,” Taguba said. But the day he got his medal “he smiled—he had a big-ass smile on his face. I’d never seen him look so proud. He was a bent man with carpal-tunnel syndrome, but at the end of the medal ceremony he stood himself up and saluted. I cried, and everyone in my family burst into tears.”

Richard Armitage, a former Navy counter-insurgency officer who served as Deputy Secretary of State in the first Bush term, recalled meeting Taguba, then a lieutenant colonel, in South Korea in the early nineteen-nineties. “I was told to keep an eye on this young guy—‘He’s going to be a general,’ ” Armitage said. “Taguba was discreet and low key—not a sprinter but a marathoner.”

At the time, Taguba was working for Major General Mike Myatt, a marine who was the officer in charge of strategic talks with the South Koreans, on behalf of the American military. “I needed an executive assistant with brains and integrity,” Myatt, who is now retired and living in San Francisco, told me. After interviewing a number of young officers, he chose Taguba. “He was ethical and he knew his stuff,” Myatt said. “We really became close, and I’d trust him with my life. We talked about military strategy and policy, and the moral aspect of war—the importance of not losing the moral high ground.” Myatt followed Taguba’s involvement in the Abu Ghraib inquiry, and said, “I was so proud of him. I told him, ‘Tony, you’ve maintained yourself, and your integrity.’ ”

Taguba got a different message, however, from other officers, among them General John Abizaid, then the head of Central Command. A few weeks after his report became public, Taguba, who was still in Kuwait, was in the back seat of a Mercedes sedan with Abizaid. Abizaid’s driver and his interpreter, who also served as a bodyguard, were in front. Abizaid turned to Taguba and issued a quiet warning: “You and your report will be investigated.”

“I wasn’t angry about what he said but disappointed that he would say that to me,” Taguba said. “I’d been in the Army thirty-two years by then, and it was the first time that I thought I was in the Mafia.”

THE INVESTIGATION

Taguba was given the job of investigating Abu Ghraib because of circumstance: the senior officer of the 800th Military Police Brigade, to which the soldiers in the photographs belonged, was a one-star general; Army regulations required that the head of the inquiry be senior to the commander of the unit being investigated, and Taguba, a two-star general, was available. “It was as simple as that,” he said. He vividly remembers his first thought upon seeing the photographs in late January of 2004: “Unbelievable! What were these people doing?” There was an immediate second thought: “This is big.”

Taguba decided to keep the photographs from most of the interrogators and researchers on his staff of twenty-three officers. “I didn’t want them to prejudge the soldiers they were investigating, so I put the photos in a safe,” he told me. “Anyone who wanted to see them had to have a need-to-know and go through me.” His decision to keep the staff in the background was also intended to insure that none of them suffered damage to his or her career because of involvement in the inquiry. “I knew it was going to be very sensitive because of the gravity of what was in front of us,” he said.

The team spent much of February, 2004, in Iraq. Taguba was overwhelmed by the scale of the wrongdoing. “These were people who were taken off the streets and put in jail—teen-agers and old men and women,” he said. “I kept on asking these questions of the officers I interviewed: ‘You knew what was going on. Why didn’t you do something to stop it?’ ”

Taguba’s assignment was limited to investigating the 800th M.P.s, but he quickly found signs of the involvement of military intelligence—both the 205th Military Intelligence Brigade, commanded by Colonel Thomas Pappas, which worked closely with the M.P.s, and what were called “other government agencies,” or O.G.A.s, a euphemism for the C.I.A. and special-operations units operating undercover in Iraq. Some of the earliest evidence involved Lieutenant Colonel Steven L. Jordan, whose name was mentioned in interviews with several M.P.s. For the first three weeks of the investigation, Jordan was nowhere to be found, despite repeated requests. When the investigators finally located him, he asked whether he needed to shave his beard before being interviewed—Taguba suspected that he had been dressing as a civilian. “When I asked him about his assignment, he says, ‘I’m a liaison officer for intelligence from Army headquarters in Iraq.’ ” But in the course of three or four interviews with Jordan, Taguba said, he began to suspect that the lieutenant colonel had been more intimately involved in the interrogation process—some of it brutal—for “high value” detainees.

“Jordan denied everything, and yet he had the authority to enter the prison’s ‘hard site’ ”—where the most important detainees were held—“carrying a carbine and an M9 pistol, which is against regulations,” Taguba said. Jordan had also led a squad of military policemen in a shoot-out inside the hard site with a detainee from Syria who had managed to obtain a gun. (A lawyer for Jordan disputed these allegations; in the shoot-out, he said, Jordan was “just another gun on the extraction team” and not the leader. He noted that Jordan was not a trained interrogator.)

Taguba said that Jordan’s “record reflected an extensive intelligence background.” He also had reason to believe that Jordan was not reporting through the chain of command. But Taguba’s narrowly focussed mission constrained the questions he could ask. “I suspected that somebody was giving them guidance, but I could not print that,” Taguba said.

“After all Jordan’s evasiveness and misleading responses, his rights were read to him,” Taguba went on. Jordan subsequently became the only officer facing trial on criminal charges in connection with Abu Ghraib and is scheduled to be court-martialled in late August. (Seven M.P.s were convicted of charges that included dereliction of duty, maltreatment, and assault; one defendant, Specialist Charles Graner, was sentenced to ten years in prison.) Last month, a military judge ruled that Jordan, who is still assigned to the Army’s Intelligence and Security Command, had not been appropriately advised of his rights during his interviews with Taguba, undermining the Army’s allegation that he lied during the Taguba inquiry. Six other charges remain, including failure to obey an order or regulation; cruelty and maltreatment; and false swearing and obstruction of justice. (His lawyer said, “The evidence clearly shows that he is innocent.”)