Battle of Kunduz
One of the bloodiest fights of the northern campaign in the Afghanistan War (2001-) was the Battle of Kunduz. Kunduz is the capital of Kunduz Province, south of Tajikistan. Converging Northern Alliance forces had taken control of Mazar-e-Sharif in Balkh Province to the west, Taloqan in Takhar Province on the east, and Pul-e-khumri in Baghlan Province to the south. On the Northern Alliance side, the commander was Abdul Rashid Dostum.
The Northern Alliance told the U.S. team, on November 10th, that Taliban were retreating into Kunduz, taking human shields. As Gary Berntsen, the CIA Special Activities Division field chief, put it, "when an Afghan who has been in combat half his life and has witnessed scores of atrocities tells you something is going to be bad, you listen." Cutting off the linkup became a high priority.  Taliban leaders in Mazir-e-Sharif had negotiated a surrender of Kunduz, with amnesty for Afghan Taliban but not for foreign fighters.  After the end of the battle, a great many Taliban and foreign fighters died; some deaths may have been due to the fog of war, while others may have been a war crime. There were two incidents involving prisoner deaths, one involving transport to the Sheberghan prison but with bodies in a grave in the Dasht-i-Leili desert, and a prison revolt at Qali-i-Jangi in Mazar-e-Sharif.
Kunduz was surrounded, and negotiations for its surrender took place at Emam Sahib on November 15. As many as 20 separate Afghan Taliban leaders were involved, each with his own following. Complicating the situation is that while the Northern Alliance would usually accept the surrender of Afghans, it often gave no quarter to foreign fighters. 
Afghan Taliban fighters surrendered at Kunduz, but foreign fighters, including Juma Namangami, a leader of the Islamic Movement of Uzbekistan, fought on. Namangami led the al-Qaeda force at Kunduz, and was killed in a U.S. airstrike; the overall Taliban commander was Mohammed Fazal. 
Kunduz fell on November 23-24; 8,000 Taliban surrendered. Amir Jhan, a former Taliban apparently accepted as a negotiator by both sides, said that after the surrender, he counted only 3,015. There are many theories for prisoner deaths, ranging from compounded errors to deliberate killing; there appear to have been miscalculations on all sides. The Northern Alliance was not prepared to handle a large number of prisoners. One of the most basic errors was failing to search all prisoners.  Jansaid that the foreign Taliban fighters from Kunduz were not supposed to surrender at Mazar-e-Sharif, but at Erganak, 12 miles west of Kunduz. "Mullah Faizal, the Taliban's commander at Kunduz, had told the foreign fighters to give up their weapons - but failed to tell them that they would then be taken into custody, it emerged from Amir Jan's account: 'The foreigners thought that after surrendering to the Northern Alliance they would be free,' he said. 'They didn't think they would be put in jail.' Dostum, however, planned to take them to "Mazar-i-Sharif's large Soviet-built airfield, but American special forces vetoed the plan, saying that the runway could be needed for military operations," according to Jan. Dostum then decided to take the prisoners to his fortress, the Qala-i-Jhangi in Mazar.
At the prison in Sheberghan prison, Physicians for Human Rights (PHR) investigators, in January 2002, found over 3000 prisoners in a facility with capacity for 800. They went there, according to Newsweek, based on a tip from International Committeee of the Red Cross personnel. The commander asked for food, supplies and a well to be dug. The prisoners, however, told the investigators they were lucky, as they had been moved from Konduz in sealed shipping containers. Many suffocated. Some survivors were later taken to Qali-i-Jhangi.
Irish filmmaker Jamie Doran has said that Special Forces took part in torture and killing, based on interviews with survivors.  There is substantial evidence that Dostum was aware of the situation, but U.S. knowledge is much less certain. Robert Young Pelton, a freelance journalist working with CNN and National Geographic, who was present, denies Doran's accusations as speculation. The two dislike one another, but both call for a forensic evaluation of the graves.  Physicians for Human Rights has filed a Freedom of Information Act suit for U.S. records on the incident. 
In 1997, PHR had, at the request of the United Nations High Commissioner for Human Rights, evaluated a number of mass graves in Afghanistan. They again went to Afghanistan January 16-21, 2002, and examined nine sites, two of which had remains consistent with recent burials, while the earlier ones were consistent with the dates of earlier battles in which the Taliban took villages in the area. The latter two were visited again, by forensic anthropologists, in February. At site #8, there was evidence that heavy machinery had been present in the area, possibly for mass burials. 
Revolt in Mazar-e-Sharif
Even before the full revolt at the Qali-i-Jangi fortress, Dostum's soldiers checked only three out of the five trucks full of prisoners for weapons. Before the full revolt a Chechen prisoner exploded a grenade, killing himself, two other prisoners, and Dostum's police chief. Later, large-scale fighting broke out when guards began tying up the prisoners. They had managed to secure 250 of the 400 detainees. The remaining prisoners - suspecting they were about to be executed - then revolted. Guardian (U.K.) correspondent Luke Harding wrote "Their fears were unwarranted: the Americans had taken pains to school General Abdul Rashid Dostam, the castle's owner, and his fellow opposition commanders that the Taliban prisoners should be treated according to international law."  Prisoners at Qala-i Jangi prison killed guards by suicide attack with hidden grenades; they were forced into cells in the basement. An American who volunteered for the Taliban, John Walker Lindh, was not yet identified. The prisoners turned on their guards; CIA officer Mike Spann was killed.
British SAS soldiers, with U.S. Special Forces, coordinated the efforts to drive out the last resisters on November 30; Dostum had variously sent burning diesel oil into the cells, but the use of chilled water forced out the last. 
CNN reporter Robert Pelton interviewed the hospitalized Lindh on December 2. Lindh explained he belonged to a Taliban auxiliary called Ansar, or "helpers", which was divided by native language of the volunteers. He said bin Laden was in charge of the Arabic-speaking part. 
- Gary Bertsen and Ralph Pezzulo (2005), JAWBREAKER: The attack on Bin Laden and al-Qaeda: A Personal Account by the CIA's Field Commander, Three Rivers Press, Crown Publishing Group, Random House, ISBN 0307351068,Berntsen, pp. 145-146
- "Fight erupts, Taliban to surrender Konduz", United Press International, November 22, 2001
- Dexter Filkins (November 15, 2001), "A NATION CHALLENGED: THE HOLDOUTS; Taliban Negotiating Surrender of Kunduz, Their Last Stronghold in Afghanistan's North", New York Times
- Berntsen, p. 242
- Luke Harding, Simon Tisdall, Nicholas Watt, Richard Norton-Taylor (December 1, 2001), "Fatal errors that led to massacre", Guardian (U.K.)
- Babak Dehghanpisheh, John Barry, Roy Gutman (August 26, 2002), The Death Convoy Of Afghanistan
- Michelle Goldberg, "Were U.S. troops in Afghanistan complicit in a massacre?", Salon.com
- Ted Rall (February 4, 2003), Adventurer Denies U.S. War Crimes in Afghanistan
- PHR Files Suit Against Defense Department in FOIA Dispute Over Documents Concerning Dasht-e-Leili Mass Grave in Afghanistan, Physicians for Human Rights, February 19, 2008
- Jennifer Leaning and John Heffernan (2002), Preliminary Assessment of Alleged Mass Gravesites in the Area of Mazar-I-Sharif, Afghanistan, Physicians for Human Rights
- Luke Harding (November 27, 2001), "Allies direct the death rites of trapped Taliban fighters", Guardian (U.K.)
- Robert Pelton (July 4, 2002), "Transcript of John Walker interview", CNN
- Berntsen, pp. 250-253