The windowless room inside the girls’ madrassa was charred, transformed from a seat of religious learning to an inferno by the suicide bomber who detonated his charge as the Pakistani commandos stormed the Red Mosque compound.

Five of the people who were sheltering inside the room were so badly burnt by the explosion that it was impossible to tell their gender or age. Yet the officer who led journalists into the site of the week-long siege said that his men had found a severed head, presumed to be that of the suicide bomber, on the floor.

In the next room, swarms of flies buzzed over the stained floor and the chunks of broken masonry where militants had built a bunker. Walls that had been painted with Islamic verses were riddled with bullet holes, evidence of a vicious 35-hour assault in which commandos fought from room to room against 70 heavily armed militants. “The resistance was beyond our expectation,” said the commander who led the siege.

Inside the madrassa, an inscription on a blackboard read: “O God give us a martyr’s death.” Another inscription, in what had been one of the biggest religious seminaries in Pakistan, read: “Even if you are alone and your enemies are in their hundreds, do not see your weakness but have faith in the Almighty.”

Thousands of women and girls, aged from 4 into their twenties, studied the Koran at the Jamia Hafsa madrassa. It is likely that the number killed during the siege will never be known. The Army said yesterday that 19 corpses were so badly burnt that they could not be identified.

The bare concrete rooms that served as classrooms and sleeping quarters were littered with broken glass and spent rifle cartridges. Books were piled into barracades, while the students’ possessions lay scattered among upturned desks.

Every part of the sprawling mosque complex was left scarred by the battle. In the blackened basement where Abdul Rashid Ghazi, the rebel cleric, and half a dozen followers made a last stand, the wall had been shattered by explosives. The acrid stench of battle hung in the air a full day after the assault. Metal furniture lay piled in a corner.

Major-General Waheed Arshad, the chief military spokesman, said that 75 militants had been killed, along with 11 soldiers in the final operation to clear the compound. Journalists were shown the remains of the militants’ deadly arsenal: machineguns, rocket-propelled grenade launchers, ammunition, antitank mines, unexploded suicide vests and a crate of petrol bombs made from green Sprite bottles. Homemade bombs, gas masks, electronic scanners and scores of alleged jihadi DVDs lay alongside them.

General Arshad said that only a few dozen of the hundreds of women and children that were said to held be inside the school were actually in the complex when the fighting began. He claimed that almost all had managed to escape.

The Red Mosque itself, or Lal Masjid, was spared the worst of the fighting. But its entrance hall was destroyed by fire and chunks of masonry were blown from the minarets, which gunmen were said to have used as a vantage point. The speakers that were used to call the faithful to prayer hung from their wires, but the towering white dome appeared unscathed.

Far from the destruction, grieving relatives and villagers buried Mr Ghazi in his ancestral village of Rohjan in southern Punjab province. His elder brother Abdul Aziz, who was caught in the early stages of the siege while trying to flee disguised as a woman, led the prayers. The cleric, who faces 25 charges of murder and terrorism, was freed on parole to attend the funeral.

Mourners smashed the glass lid of the coffin and tore a white cloth from the corpse’s face to see for themselves that it was Mr Ghazi. There were chants of “al-Jihad, al-Jihad” as prayers were read for the rebel leader. “Hundreds of our mothers, sisters, sons and daughters have rendered sacrifices,” the cleric declared before leading prayers attended by about 2,000 people.

Almost 70 others killed in the raid were interred without ceremony in unmarked graves in Islamabad. A cleric read verses from the Koran, although full funeral rites were not observed. There were no names on the coffins, only number codes.

President Pervez Musharraf, in a televised address to the nation, said that his Government was determined to take the fight against extremism to its conclusion.

Anger at the Government’s action ran deep in tribal parts of northwest Pakistan. At least seven people, including three policemen, were killed in two separate blasts, one of them a suicide bomb attack on a senior government official. Police officials said that the attacks were in retaliation to the killing of Mr Ghazi.

Cost of defiance

75: defenders were killed during the assault

39: of the dead could be confirmed as being under 18

19: of them are “beyond recognition and they could be anybody, any gender, any age”, according to Major-General Waheed Arshad, Pakistani military spokesman

11: soldiers died storming the mosque

2: undetonated explosive vests were reported found by attackers, with machineguns, grenade launchers, rifles and ammunition

2,000: supporters attended the funeral of Abdul Rashid Ghazi, the mosque rebels’ leader, killed in final attack

Source: agencies; Times archive

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