AMERICAN VICEROY.(Zalmay Khalilzad)

One afternoon in mid-October, Zalmay Khalilzad, the American Ambassador to Iraq, received a visitor in his office at the United States Embassy in Baghdad. The Embassy, housed in Saddam Hussein's old Republican Palace, is a warren of high-ceilinged rooms, great halls, and stairways, decorated in onyx and marble. The United States has established a paramilitary bureaucracy inside; its scale and its purposeful, nononsense atmosphere are reminiscent of the Pentagon. With five thousand employees and contractors, the Embassy is the true locus of power in Iraq. Khalilzad's visitor was Falah al-Naqib, a Sunni Arab who had been Iraq's interior minister in the pro-American government of Iyad Allawi until its defeat, in last January's elections, by a coalition of Shiite religious parties. Naqib had come to Khalilzad, as many Iraqi politicians do, because he had an urgent problem to discuss.

Naqib told Khalilzad that he had a document showing that his successor at the interior ministry, Bayan Jabr, had ordered the arrests of sixteen Sunni men who were later found executed. He said that Jabr had also detained the son of a friend of his, for what he believed were political reasons. For months, there had been reports that newly formed interior-ministry brigades were carrying out death-squad-style operations in and around Baghdad--assassinating insurgent suspects, usually Sunnis. Jabr, a senior official in the Supreme Council for Islamic Revolution in Iraq (SCIRI), had recruited a large number of militiamen from the group's military wing, the Badr organization, into the government security forces. Naqib said that he believed the militias were a greater long-term problem than the insurgency, and he wanted Khalilzad to do something about it.

Khalilzad raised his eyebrows with interest, and signalled to an aide, who sat in a corner of the room taking notes. He acknowledged that militias were a problem. "They are the underpinnings of a future civil war, or of warlordism," he told Naqib. He said that he planned to institute a program to get members of the militias off the street and into paying jobs. But his immediate concern was terrorists crossing the Syrian border into Iraq.

Khalilzad is accredited to the new Iraqi government, but, with the backing of a hundred and sixty thousand U.S. troops, he often seems to be the one holding the government together. His position is more like that of a viceroy or an imperial high commissioner than that of a traditional diplomat. And the conflict he is dealing with is increasingly sectarian. Ever since the U.S. invasion, in March of 2003, the minority Sunni Arabs, who were favored under Saddam Hussein, have felt disenfranchised by the shift in power to the Shiites. The Iraqi insurgency is largely Sunni, as are the foreign jihadi suicide bombers. Their primary victims, along with American soldiers, are Shiites, just as the victims of the Shiite gunmen and American soldiers are mostly Sunnis.

A few weeks after Naqib's visit, I accompanied Khalilzad on a night flight out of Baghdad, headed for a conference in Vienna. On the plane, a military turboprop, an aide produced several paper bags bearing the Subway-sandwich logo; the chain has an outlet inside the Green Zone, the heavily protected area where the Embassy and Iraq's government are situated and where most foreigners in Iraq live. Khalilzad is long-bodied and long-faced. He has hooded brown eyes, a large aquiline nose, and a strong jaw. He dresses sharply, favoring black or charcoal-gray business suits. He is fifty-four and walks with the loose-limbed saunter of a basketball player. As we ate, he told me that the previous night American troops had raided an interior-ministry building and discovered a hundred and seventy-three prisoners being held secretly in a basement cell. (The story appeared the next day on the front pages of newspapers around the world.) Many of the prisoners were malnourished or very sick, and showed signs of torture. Khalilzad said that the soldiers had found instruments of torture, including whips and metal cables, which he'd been shown in his office earlier that afternoon. "It was pretty bad," he said.

Khalilzad has a reputation both as a strategic thinker and as an operator, a man with extraordinary political instincts, and the attention given to the raid on the prison did not seem to be accidental. When he told me about what the soldiers had found, it was clear that he had been prepared for the discovery, and that he had worked out the steps of his response in advance. The story looked like a disaster for the Bush Administration: the war had been justified (at least in retrospect) as a way of bringing democracy to Iraq; now, it seemed, the U.S. was propping up a government that used the same tactics against its opponents as Saddam had. But Khalilzad wasn't unduly concerned; instead, he tried to spin the discovery as a good thing, because it would send a message to the Sunni community that the Americans were intervening on their behalf. It would also let the Shiites in the government know that there were limits to their power, which America was willing to enforce.

In the publicity surrounding the interior ministry's secret prison, Sunni politicians were at the forefront of those denouncing the government. Since the war began, Sunnis generally have been perceived as Baathists, disgruntled tribalists, or Islamist terrorists. (And in fact Naqib, for all his expressions of outrage, has been accused of allowing torture when he was in office.) This was one of the first times that the Sunnis had been able to claim convincingly that they were the victims, and by doing so they had gained a new legitimacy. That opportunity had been managed by the American representative in Iraq and an enemy of the Sunni insurgency--Zalmay Khalilzad.