In Afghanistan last November, the Northern Alliance, supported by American Special Forces troops and emboldened by the highly accurate American bombing, forced thousands of Taliban and Al Qaeda fighters to retreat inside the northern hill town of Kunduz. Trapped with them were Pakistani Army officers, intelligence advisers, and volunteers who were fighting alongside the Taliban. (Pakistan had been the Taliban’s staunchest military and economic supporter in its long-running war against the Northern Alliance.) Many of the fighters had fled earlier defeats at Mazar-i-Sharif, to the west; Taloqan, to the east; and Pul-i-Khumri, to the south. The road to Kabul, a potential point of retreat, was blocked and was targeted by American bombers. Kunduz offered safety from the bombs and a chance to negotiate painless surrender terms, as Afghan tribes often do.

Surrender negotiations began immediately, but the Bush Administration heatedly—and successfully—opposed them. On November 25th, the Northern Alliance took Kunduz, capturing some four thousand of the Taliban and Al Qaeda fighters. The next day, President Bush said, “We’re smoking them out. They’re running, and now we’re going to bring them to justice.”

Even before the siege ended, however, a puzzling series of reports appeared in the Times and in other publications, quoting Northern Alliance officials who claimed that Pakistani airplanes had flown into Kunduz to evacuate the Pakistanis there. American and Pakistani officials refused to confirm the reports. On November 16th, when journalists asked Secretary of Defense Donald Rumsfeld about the reports of rescue aircraft, he was dismissive. “Well, if we see them, we shoot them down,” he said. Five days later, Rumsfeld declared, “Any idea that those people should be let loose on any basis at all to leave that country and to go bring terror to other countries and destabilize other countries is unacceptable.” At a Pentagon news conference on Monday, November 26th, the day after Kunduz fell, General Richard B. Myers, of the Air Force, who is the chairman of the Joint Chiefs of Staff, was asked about the reports. The General did not directly answer the question but stated, “The runway there is not usable. I mean, there are segments of it that are usable. They’re too short for your standard transport aircraft. So we’re not sure where the reports are coming from.”

Pakistani officials also debunked the rescue reports, and continued to insist, as they had throughout the Afghanistan war, that no Pakistani military personnel were in the country. Anwar Mehmood, the government spokesman, told newsmen at the time that reports of a Pakistani airlift were “total rubbish. Hogwash.”

In interviews, however, American intelligence officials and high-ranking military officers said that Pakistanis were indeed flown to safety, in a series of nighttime airlifts that were approved by the Bush Administration. The Americans also said that what was supposed to be a limited evacuation apparently slipped out of control, and, as an unintended consequence, an unknown number of Taliban and Al Qaeda fighters managed to join in the exodus. “Dirt got through the screen,” a senior intelligence official told me. Last week, Secretary of Defense Rumsfeld did not respond to a request for comment.

Pakistan’s leader, General Pervez Musharraf, who seized power in a 1999 coup, had risked his standing with the religious fundamentalists—and perhaps his life—by endorsing the American attack on Afghanistan and the American support of the Northern Alliance. At the time of Kunduz, his decision looked like an especially dangerous one. The initial American aim in Afghanistan had been not to eliminate the Taliban’s presence there entirely but to undermine the regime and Al Qaeda while leaving intact so-called moderate Taliban elements that would play a role in a new postwar government. This would insure that Pakistan would not end up with a regime on its border dominated by the Northern Alliance. By mid-November, it was clear that the Northern Alliance would quickly sweep through Afghanistan. There were fears that once the Northern Alliance took Kunduz, there would be wholesale killings of the defeated fighters, especially the foreigners.

Musharraf won American support for the airlift by warning that the humiliation of losing hundreds—and perhaps thousands—of Pakistani Army men and intelligence operatives would jeopardize his political survival. “Clearly, there is a great willingness to help Musharraf,” an American intelligence official told me. A C.I.A. analyst said that it was his understanding that the decision to permit the airlift was made by the White House and was indeed driven by a desire to protect the Pakistani leader. The airlift “made sense at the time,” the C.I.A. analyst said. “Many of the people they spirited away were the Taliban leadership”—who Pakistan hoped could play a role in a postwar Afghan government. According to this person, “Musharraf wanted to have these people to put another card on the table” in future political negotiations. “We were supposed to have access to them,” he said, but “it didn’t happen,” and the rescued Taliban remain unavailable to American intelligence.

According to a former high-level American defense official, the airlift was approved because of representations by the Pakistanis that “there were guys— intelligence agents and underground guys—who needed to get out.”

Once under way, a senior American defense adviser said, the airlift became chaotic. “Everyone brought their friends with them,” he said, referring to the Afghans with whom the Pakistanis had worked, and whom they had trained or had used to run intelligence operations. “You’re not going to leave them behind to get their throats cut.” Recalling the last-minute American evacuation at the end of the Vietnam War, in 1975, the adviser added, “When we came out of Saigon, we brought our boys with us.” He meant South Vietnamese nationals. “ ‘How many does that helicopter hold? Ten? We’re bringing fourteen.’ ”

The Bush Administration may have done more than simply acquiesce in the rescue effort: at the height of the standoff, according to both a C.I.A. official and a military analyst who has worked with the Delta Force, the American commando unit that was destroying Taliban units on the ground, the Administration ordered the United States Central Command to set up a special air corridor to help insure the safety of the Pakistani rescue flights from Kunduz to the northwest corner of Pakistan, about two hundred miles away. The order left some members of the Delta Force deeply frustrated. “These guys did Desert Storm and Mogadishu,” the military analyst said. “They see things in black-and-white. ‘Unhappy’ is not the word. They’re supposed to be killing people.” The airlift also angered the Northern Alliance, whose leadership, according to Reuel Gerecht, a former Near East operative for the C.I.A., had sought unsuccessfully for years to “get people to pay attention to the Pakistani element” among the Taliban. The Northern Alliance was eager to capture “mainline Pakistani military and intelligence officers” at Kunduz, Gerecht said. “When the rescue flights started, it touched a raw nerve.”

Just as Pakistan has supported the Taliban in Afghanistan, Pakistan’s arch-rival India has supported the Northern Alliance. Operatives in India’s main external intelligence unit—known as RAW, for Research and Analysis Wing—reported extensively on the Pakistani airlift out of Kunduz. (The Taliban and Al Qaeda have declared the elimination of India’s presence in the contested territory of Kashmir as a major goal.) RAW has excellent access to the Northern Alliance and a highly sophisticated ability to intercept electronic communications. An Indian military adviser boasted that when the airlift began “we knew within minutes.” In interviews in New Delhi, Indian national-security and intelligence officials repeatedly declared that the airlift had rescued not only members of the Pakistani military but Pakistani citizens who had volunteered to fight against the Northern Alliance, as well as non-Pakistani Taliban and Al Qaeda. Brajesh Mishra, India’s national-security adviser, said his government had concluded that five thousand Pakistanis and Taliban—he called it “a ballpark figure”—had been rescued.