Exclusive: Cairo at war - under siege inside the Al-Fath Mosque

Yasmine Ahmed's two brothers had been trapped in the siege for over 12 hours. Packed into a sweltering back room barricaded with chairs and wooden tables, they had been cooped up alongside hundreds of panicking Islamists and the decomposing corpses from another weekend of violence.

Away from the besieged protesters, down a corridor and inside the main prayer hall of the mosque, an army commander huddled in a circle with his troops. Standing on the grubby carpet littered with discarded shreds of cotton wool and surgical pads, his face was slick with sweat.

Hundreds of locals were crammed against the pointed steel gates of the mosque courtyard. Many were in no mood to forgive those trapped inside; in the minds of some Egyptians, the Morsi supporters have become little more than "terrorist" outlaws.

"Their fate is not in my hands now," said Yasmine, 20, a college student. "The army and the police think the people trapped inside are terrorists. But they are not. What we have now is chaos. There is chaos between all the Egyptian people."

The fear and anxiety were palpable. Weeping relatives tramped around the prayer hall, while jumpy police officers toted their Kalashnikovs in one hand, wide-eyed and frantically chewing gum.

Adding to the sense of confusion, dozens of civilians had also managed to gain access to the building. All the while, hundreds of Morsi supporters – who had sought sanctuary in the mosque following the gunfights that erupted in nearby Ramses Square on Friday – shouted and yelled out from behind their barricades.

At around 12.40pm, the situation suddenly deteriorated. Heavy bursts of gunfire began crackling outside the mosque. "It's the Muslim Brothers," shouted a boy in his late teens. "They're firing at us from above."

Panic gripped the prayer hall. Dozens of black-clad men from the security services ran for shelter under the windows of the eastern wall. Others squatted behind thick pillars as the live rounds swooshed around outside the mosque.

One policeman ran to prod his gun through a smashed window in the western wall. His darting eyes searched for the source of the shooting. Seeing no target, he stepped away.

Suddenly a squad of armed police dashed to the corridor leading to the barricaded back room and lined themselves against the wall. Pointing their gun barrels skyward, they poised themselves to end the siege. Groups of civilians, relatives and other armed police ran to take cover next to the eastern wall.

Just then someone pointed to the windows on a second floor overlooking the prayer hall. "There are people upstairs," he screamed. A moment later there was a flash and a small explosion in the centre of the room. Soldiers and civilians started screaming. A cloud of pale smoke dissipated around the hall.

Seconds later there was another loud boom, this time from the direction of the corridor leading towards the barricaded Islamists. Panic erupted as those inside the mosque began fleeing for the door. A senior police officer ordered people to leave, furiously waving an arm as he stomped through the prayer hall with a Kalashnikov in his right hand.

Outside, the scores of civilians who had gained access to the main courtyard cowered against the mosque walls as heavy bursts of live ammunition clattered around Ramses Square. Eyewitnesses reported seeing gunshots being fired from the mosque's minaret.

Amid the fear and confusion, angry civilians mobbed foreign journalists who had been reporting on the siege. One Western reporter was briefly knocked unconscious after being clubbed over the head with a stick. Soldiers fired shots in the air to scare away the attackers.

At least two journalists were rescued from angry locals by troops stationed in Ramses Square. Other reporters were also arrested or detained in Cairo yesterday. The Muslim Brotherhood, which won the presidency last year after decades of repression, looks in danger of being expunged again from Egypt's political life. Yesterday it was reported Egypt's Prime Minister Hazem el-Beblawi has proposed disbanding the Muslim Brotherhood, raising the prospects of large-scale arrests if membership becomes outlawed.

It was also reported that Egyptian security forces yesterday arrested the brother of al-Qa'ida chief Ayman al-Zawahiri. Mohammed al-Zawahiri, leader of the ultraconservative Jihadi Salafist group, was detained at a checkpoint in Giza. Said to be an ally of ousted President Morsi, Mohammed al-Zawahiri is accused of commanding Islamic insurgents in the Sinai peninsula.

The interim government, backed by an apparently irrepressible military establishment, has initiated a bloody war on political Islam. Successive massacres over the past six weeks have been so astonishingly brutal that nobody knows exactly how many people have been killed.

Even taking the conservative estimates of health officials, the bloodletting points to a country that is ripping itself apart. At least 600 dead after Wednesday's massacre of Morsi supporters; more than 170 on Friday; hundreds more since the popular coup greeted with such jubilation by some on 4 July.

Nobody has been safe. Among the dead during Friday's violence was Ammar Badie, the son of the Brotherhood's Supreme Guide. On Wednesday, the daughter of Mohamed el-Beltagi, a leading Brotherhood official, was killed during the massacre. Mostafa Yacoub, said he had known 17-year-old Asmaa el-Beltagi and that she had grown distant from the Brotherhood ideology espoused by her father.

During violent demonstrations at the end of 2011 he said Asmaa had shared the streets with liberal and secular protesters who were battling the central security forces.

"She was young and wanted to develop her own thoughts," said Mr Yacoub. "She did a lot of community work. She wanted to be open to other sides of society." Those hopes were exterminated on Wednesday when police bullets shredded the Islamist encampment in eastern Cairo.

Islamists have responded to the recent violence by attacking churches, Christian homes and businesses.

The attacks confirm what many liberals have long suspected – that followers of political Islam are agents of intolerance and not fit to enjoy power in Egypt.

Yesterday's reports that the authorities are considering ways to consign the Brotherhood to political oblivion are a natural consequence of such sentiment.

It is hoped that Egypt's deputy prime minister will propose a possible way out of the bloody confrontation when the cabinet discusses the crisis today.

Foreign Secretary William Hague has condemned the "disproportionate use of force" by the Egyptian security forces as he issued a fresh appeal to all sides to end violence.

In Cairo, the city that breathes with a bustling vivacity, it feels as if it has died a death of sorts. As a result of the new 7pm curfew, the city centre is enveloped in a deathly pall of quiet by nightfall.

The roads that would usually be bursting with street hawkers and honking drivers are empty. Volunteers staffing civilian "checkpoints" – usually little more than a steel road barrier dragged into the street – check car boots and rummage through the passengers' rucksacks.

For its 17 million inhabitants, the city can rarely have felt so alien. For the political map-makers of Egypt's tortured transition, the future can hardly have seemed less certain.