The region of Aqtash, which lies east of the M.S.F. hospital in Kunduz city, contains some two dozen villages of mud and stone. Standing at the main intersection there four years ago, I could see six or seven flags perched atop various houses, each marking the territory of different anti-Taliban militias that had been created by the Afghan government and the United States. It was harvest season, the time of year when the militiamen go house to house demanding taxes and food. Earlier, one group had erected a checkpoint on the road leading into a village; not to be outdone, rival groups began setting up checkpoints of their own. To reach the main bazaar, you would have to pass up to a dozen checkpoints, surrendering a transit fee at each. That morning, the turf jostling spilled over into direct conflict. Two anti-Taliban groups opened fire on each other, reportedly leaving three dead.

Under the circumstances, people stayed home unless absolutely necessary, but even the indoors was no refuge. The week before, I was told that a militia fighter, who was part of the U.S. program to train and equip anti-Taliban militias, had broken into someone’s house. “He found a girl alone in there and raped her,” Muhammad Hafiz, his commander, told me. “He escaped and we don’t know where he went.” Hafiz promised an investigation. Families were loathe to let women out of sight. Girls stopped going to school, but being a boy didn’t always help. When visiting a militia compound, I learned from villagers that a boy had recently been brought onto the base to spend the night. The commander at the compound is said to have denied it, but later one of his fighters was more forthcoming. “The Taliban used to throw bodies in the river,” he told me. “We were just having fun.”

A few months after my visit, I was told the anti-Taliban militias of Aqtash erupted in clashes again when one commander kidnapped a bacha ba-rish, a boy sex slave, belonging to another group. Seven were killed and many more wounded. In time, families with access to weapons began arming themselves to protect against the militias. Some, who could afford it, tried to flee. And others, especially Pashtuns, invited the Taliban into their village as protection.

When the Taliban marched victoriously through Kunduz city last month, calling out from their loudspeakers for locals to stay indoors and not resist, people mostly listened—not because they support the Taliban, but because the alternative, a collection of strongmen and militias masquerading as a state, was simply not worth dying for. It was this deep-seated anger and a dysfunctional warlord politics that pitted Kunduz government elites against each other, that allowed the momentary fall of a provincial capital to the insurgency for the first time in 14 years. In the end, the Taliban were unable to hold Kunduz—the group announced its full retreat on Tuesday—but the police that caused the city’s downfall remain in place.

It would seem, at first blush, that Kunduz is an unlikely spot for the Taliban’s resurgence. In the 1990s, Tajik, Uzbek, and Turkmen villages suffered greatly under Taliban rule, but instead of rectifying that injustice, the U.S. intervention merely reversed the pattern of abuse. By 2002, human-rights organizations were recording widespread attacks against Pashtuns by U.S.-backed Afghan security forces. “The Taliban did the crimes,” a Pashtun elder told Human Rights Watch, “but the punishment was for us.”

The Taliban exploited the disaffection, and by 2009 the group was pressing at the gates of Kunduz city. Panic spread in official circles, and the National Directorate of Security, Afghanistan’s spy agency, began slipping weapons and funds to erstwhile Northern Alliance figures. The U.S., eager to replicate the Anbar Awakening in Iraq, soon got in on the act, creating militias of its own, resulting in an alphabet soup of militia programs: the A.L.P., the C.I.P., the A.P.P.F., all little more than euphemisms for irregular armed groups. The U.S. seemed uninterested in what these newly created strongmen stood for, only in what they claimed to stand against—the Taliban. (An American Embassy cable published by WikiLeaks described one such strongman, Mir Alam, who would become a key ally of U.S. forces, as engaging in “a broad range of criminal activity, including extortion, bribery, and drug trafficking.”)

In 2011, I spent three weeks living with the militias of Kunduz in order to see what this experiment meant for Afghanistan’s future. By then, the province, which is the size of New Jersey, had nearly 100 official and unofficial militias, making it the most heavily militarized place in the country. Some of those I met had joined a militia to protect their families against Taliban brutality, some out of a desire for wealth, others for power. But mostly—because people don’t come in neat analytical packages—it was some combination of these factors.

Whatever their reasons for joining, enterprising men used Western guns and money to attract followers. In Aqtash, local strongman Mir Alam began recruiting in Tajik villages, until he amassed nearly a dozen armed groups under his command. In response, a commander named Mohammad Omar, whom locals called Pakhsaparan, the wall crusher, began building up a private army of his own by drawing recruits from Pashtun villages. Another commander founded a force of Hazaras. During my visit, someone placed an I.E.D. in front of Commander Omar Pakhsaparan’s compound, nearly killing dozens of civilians. He reported the incident to Kabul as a Taliban bomb, but privately he believed it to be the work of a rival commander. The next day, locals told me, they attacked the rival militia’s village, setting a number of shops ablaze. Weeks later, locals allege, the rivals retaliated by kidnapping and raping a boy from a village under Pakhsaparan’s control.

Last year, President Ashraf Ghani appointed a new governor and earlier this year delivered a mandate to dismantle the militias, but it proved too little loo late, as strongman networks had infected the highest echelons of Kunduz government. As Bethany Matta reported for the Afghanistan Analysts Network, the new governor was at odds with his own deputy, who told the AFP, “There is no such thing as good militia or bad militia. Any militia fighting the Taliban are good.” Meanwhile, the chief of police, who reportedly has ties to Mir Alam, refused government orders to arrest militia leaders. The commander of one of the largest militias in the province has a brother who is the speaker of the Afghan parliament, while his on-again, off-again rival has relatives in the Ministry of Interior.

In this environment, the Taliban flourished. Leaflets would appear in militia-ravaged villages promising Taliban law and order. Insurgents assassinated some militia commanders and co-opted others; a U.S. Embassy cable noted that some militias were cooperating with both insurgents and the Afghan government, “changing their behavior opportunistically depending on their own interests.” Some militias proved more interested in rape and tax collection than fighting the insurgents, and when the Taliban made pushes, these groups fled. One village after the next began to fall. By August, insurgents had succeeded in bringing the majority of Aqtash and other regions near the provincial capital under their control.

Ultimately, the Taliban proved unified enough to take Kunduz city, but not strong enough to hold it. It was a symbolic victory for the insurgency and a blow for the government and America’s legacy; on Thursday, President Obama announced that he was halting the withdrawal of U.S. troops from Afghanistan. But the true losers, as always, are the ordinary men and women of Kunduz. After the M.S.F. air strike, I called a friend in Kunduz to check up on him. “The Taliban came into the city and said they were liberating us, and the Americans say they are liberating us with their bombs,” he said. “We don’t want any more liberation.”

Anand Gopal is the author of No Good Men Among the Living: America, the Taliban, and the War Through Afghan Eyes.