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A single, horrific, atrocity has provided a defining moment in every war of the modern age. America is still facing demands to apologize for the 1968 My Lai massacre in Vietnam , while the remains of charred Iraqi soldiers on the Mutla Ridge, outside Kuwait, provided a chilling illustration of Washington’s overwhelming firepower during the Gulf war.

Questions are being asked about whether the bloody end to this week’s prison siege at the 19th-century Qala-i-Jangi, outside Mazar-i-Sharif, will provide the defining moment of the Afghan war. Pictures of aid workers picking their way through the corpses of hundreds of Taliban prisoners, killed by a combination of US bombing and Northern Alliance savagery, have caused revulsion around the world.

As pressure grows on Britain and the US to hold an inquiry into the killings, Guardian has pieced together a minute-by-minute account of this week’s events. This suggests that from the very first, when Taliban soldiers fell into the hands of the Alliance after the fall of Kunduz, a series of catastrophic errors were made.

Amir Jan, a Pakhtoon commander who defected to the anti-Taliban opposition earlier this year, said that the elite foreign fighters from Kunduz were never supposed to turn up in Mazar-i-Sharif, Afghanistan’s main northern city.

The foreigners – Arabs, Pakistanis, Chechens and Uzbeks – were meant to surrender at Erganak, a mountainous frontline position 20kms west of Kunduz. Instead, they travelled across the desert through the night and arrived on the outskirts of Mazar, in a wilderness of desert and telegraph poles, at 3am last Saturday.

Mullah Fahzel, the Taliban’s commander at Kunduz, had instructed the foreign fighters to give up their weapons – but failed to tell them that they would then be taken into custody. “The foreigners thought that after surrendering to the Northern Alliance they would be free,” Jan said. “They didn’t think they would be put in jail.”

While US soldiers dressed in desert khaki set up satellite links, soldiers loyal to the alliance warlord General Rashid Dostam took up attack positions. After three to four hours’ negotiation, the Taliban fighters agreed to surrender again – but only to Amir Jan, whom they trusted because of his Pakhtoon roots and Taliban history. Dostam’s militia then began disarming the Taliban fighters and piling their weapons into a green lorry.

Dostam had arranged to take the prisoners to Mazar-i-Sharif’s large Soviet-built airfield, well away from the centre of the city. But American special forces vetoed the plan, saying that the runway could be needed for military operations, Jan revealed.

Instead, Dostam would take the prisoners to his own personal fortress on the muddy outskirts of Mazar-i-Sharif, the Qala-i-Jangi. Over the previous two weeks several American officers had secretly spent many hours in the castle. They knew it was full of heavy weaponry.

Nonetheless, they agreed with Dostam’s impromptu scheme. By mid-afternoon on Saturday, the prisoners had been piled into five trucks. Said Kamal, Dostam’s head of security, arranged for prisoners in the first three trucks to be body searched. But with dusk approaching, the convoy set off with the last two trucks not searched. This proved to be disastrous.

While Dostam set off with the bulk of his army towards Kunduz, the convoy rolled the other way into the Qala-i-Jangi, where a comparatively small number of guards had been left behind. Nader Ali, Dostam’s chief of police, made another attempt to search the prisoners soon after they arrived in late afternoon. As he was about to be frisked a Taliban fighter detonated a hidden grenade killing himself, Ali and another Dostam aide.

While the dying Ali was carried away, soldiers then bundled the Taliban fighters into the stable area to the north of the compound. The search was abandoned.

That night eight of Osama bin Laden’s fighters blew themselves up in a room in the prisoners’ compound, Jan said. It soon became clear that a large minority of the Taliban were still armed with grenades. “After that I decided they were hardliners, that they were dangerous,” Jan added. “We agreed it would be better to tie up their hands and put them in the basement.”

The following morning (Sunday) guards prepared to implement the new order. At the same time Simon Brooks, the head of the International Committee for the Red Cross in northern Afghanistan, swept into the Qala-i-Jangi in his white Red Cross vehicle. He had come to seek reassurances from Kamal that the prisoners would be treated humanely. The Red Cross also wanted to register the prisoners’ names and allow them to send a message back to their families. Brooks was not the only person interested in the new Arab, Pakistani and Chechen detainees.

CIA AGENTS: Two CIA agents, Johnny “Mike” Spann and “Dave”, had also been instructed to screen the Taliban fighters for possible links with al-Qaida. From a distance Dave looked Afghan. He even spoke Uzbek, the language of Dostam’s soldiers, and wore a shalwar kameez beneath a long coat. But his square-cropped haircut gave the game away, and revealed him as an American.

Two television crews – from Reuters and the German station ARD – had also turned up at the fort. They were in the prisoners’ compound, together with Dave and Mike, who had begun interviewing suspects.

At 11:25am the Taliban fighters were marched to the central grassy compound of their mini-citadel. The guards tied up the first eight prisoners, Jan said. “The prisoners suspected they were about to be shot. They attacked one of the guards and grabbed his gun,” he added. The foreign fighters had also assumed that the television journalists were American soldiers who had come to film their execution.

Another prisoner grabbed Mike and set off a grenade, blowing him up. This conflicts with the CIA account of his death which says that he was shot.

All hell then broke loose: the prisoners shot dead five guards and grabbed their weapons, while the journalists ran for cover. Dave only managed to escape by shooting dead at least one Taliban prisoner with his pistol. A firefight blew up between the prisoners, now in charge of their own fortified area, and soldiers sitting in Dostam’s headquarters building 300 metres away, down a line of trees.

“Dave managed to reach the rooftop [of Dostam’s HQ] about 15 minutes after fighting broke out,” Brooks said. “One of the Taliban who had obviously been wired with explosives simply grabbed the other American and the bomb detonated.”

“I met Dave in the building. He was absolutely completely shocked and really quite scared. I can now understand why: he witnessed his friend being blown up. He had managed to shoot his way out and run 150 metres out of the building.”

Soon the firefight had developed into a major battle, as the Taliban prisoners broke into the arms depot in their compound and helped themselves to mortars and rocket launchers. From the rooftop, Dave borrowed a satellite phone from the German television crew and phoned the American embassy in Uzbekistan.

“We have lost control of the situation. Send in helicopters and troops,” he said.

The call appeared to work. As the Red Cross vehicle blazed in the car park, and Brooks slithered down the mud battlements to safety, the Pentagon prepared to send in the airforce. Most of the eight prisoners who had been tied up when the battle broke out were shot dead in the early minutes; the others were able to take cover. Their bodies were still there four days later when Dostam’s troops were finally able to re-enter the compound.

At 3:30pm the jets dispatched by the Pentagon fired nine or 10 missiles directly into the Taliban’s positions. All of them hit their target – apart from the last one, which sank into a field more than one kilometre away. In the confusion, a small group of at least 10 prisoners escaped.

The following day the remaining Taliban, some armed with rocket launchers, held out as B-52 bombers flew repeatedly overhead. Alarmed by the resilience of the Taliban fighters, further special forces arrived at the base on Tuesday. They reportedly advised the alliance to flush out the remaining Taliban by pouring oil into the basement and setting fire to it.

It took a tank and an intensification of bombings from the air to finish them off.

Confident that the way was clear, the alliance regained control of the fortress on Wednesday. But on Thursday it emerged that a lone Taliban was still holed up in a basement of the fortress where he was surviving on horse meat.

High above the lone survivor, the imposing figure of Dostam toured the fortress where the full horror of the siege was on display. A photographer saw the bodies of up to 50 Taliban fighters, whose hands had been bound by scarves, laid out in a field in the southern part of the fort. The photographer watched as alliance fighters cut the scarves from the hands of some of the corpses; at least one picked gold fillings from a corpse.

WAR CRIMES: As Washington attempted to wash its hands of the episode, saying that the alliance was responsible for the prisoners, human rights lawyers warned that the Geneva convention may have been breached on two counts. This is over the degrading treatment of the Taliban, when they were tied up, and the huge firepower directed at them by US warplanes.

On the first count, article 13 of the convention says: “Prisoners of war must at all times be humanely treated.” On the second count, the convention permits the use of force against prisoners. But it says that this must be proportionate.

Christopher Greenwood, professor of international relations at the London School of Economics and joint editor of International Law Reports, said that killing people with hands tied behind their backs was illegal. “If it was heavy-handed overreaction, it was illegal,”, he said.

Amid the doubts about the legality of the US and alliance response, there were also questions about the conduct of the two CIA officers. Adam Roberts, professor of international relations at Oxford University and a leading authority on the laws of war, described their conduct as “incredibly stupid and unprofessional”.

Angered by the death of Spann – the first American to die in the conflict – CIA director George Tenet swept aside the criticism as he accused the Taliban of premeditated murder.

“Their prison uprising – which has murder as its goal – claimed many lives, among them that of a very brave American,” he said of Spann, who worked in the directorate of operations, which analysts say is involved in “paramilitary” activities.

As the final bodies are cleared, the battle has now moved to Britain and America, where both governments have rejected calls by Amnesty International for an inquiry. Amnesty hit back, saying that this raised questions about their commitment to the rule of law.