In the early hours of 8 July 2013, 51 Muslim Brotherhood supporters camped outside the Republican Guards' club in Cairo were killed by security forces. The Egyptian military claimed the demonstrators had attempted to break into the building with the aid of armed motorcyclists.

After examining video evidence and interviewing eyewitnesses, medics and demonstrators Patrick Kingsley finds a different story – a coordinated assault on largely peaceful civilians. 'If they'd just wanted to break the sit-in, they could have done it in other ways. But they wanted to kill us,' a survivor says

At 3.17am on Monday 8 July, Dr Yehia Moussa prepared to kneel outside the Republican Guards' club in east Cairo for dawn prayers. For a few more short hours, Moussa would remain the official spokesman for the Egyptian health ministry. But he was outside the club that day in a personal capacity. Along with about 2,000 supporters of the Muslim Brotherhood, Moussa had camped outside the gated compound in protest at the removal of ex-president Mohamed Morsi, who they then believed was imprisoned inside.

Like everyone else, Moussa knelt with his back to the barbed wire fence protecting the entrance to the club. A few feet away were Dr Reda Mohamedi, an education lecturer at al-Azhar University, and beyond him Dr Yasser Taha, an al-Azhar biochemistry professor. All three were friends from university days, and had shared a tent that night.

Within the hour, Taha would be dead with a bullet in his neck and Mohamedi would be unconscious, a bullet through his thigh. Moussa would have gunshot wounds in both legs and be missing most of his right index finger.

All three were victims of Egypt's bloodiest state-led massacre since the fall of Hosni Mubarak, in which, according to official figures, at least 51 people were killed by Egyptian security forces and at least 435 injured. Two policemen and one soldier were also killed with 42 injured. The military has said that the assault on the protesters was provoked by a terrorist attack. At about 4am, according to the army's account, 15 armed motorcyclists approached the Republican Guards' club compound. The army said that the motorcyclists fired shots, that people attempted to break into the compound, and that the soldiers then had no choice but to defend their property.

However, a week-long investigation – including interviews with 31 witnesses, local people and medics, as well as analysis of video evidence – found no evidence of the motorcyclist attack and points to a very different narrative, in which the security forces launched a co-ordinated assault on a group of largely peaceful and unarmed civilians.

The army turned down four requests to interview soldiers present at the scene.

A spokesman did provide footage of at least three pro-Morsi supporters using some form of firearm some time after the start of the massacre. But the earliest act of provocation the army has been able to prove – a protester throwing stones – comes at 4.05am, more than half-an-hour after most witnesses agree the camp came under attack.

3.17am
Call to prayers

Many of the Morsi supporters gathered outside the Republican Guards headquarters shortly after 3am on Monday had been camped there since the previous Friday. They had blocked off the road – Salah Salem Street, one of Cairo's main thoroughfares – and set up tents. On the first day of the sit-in, three protesters had been shot dead by state officials. But by 3.17am on Monday, when the imam called the camp to prayer, all was calm. Women and children strolled among the tents. A platoon of soldiers stood idly behind the barbed wire fence. A few dozen protesters manned the barricades the pro-Morsi demonstrators had erected on either side of the sit-in, 300 metres up the road in both directions. Others were still asleep. But most gathered to pray – filling the junction between Salah Salem Street and Tayaran Street, the half-mile-long side street that leads all the way to the Rabaa al-Adawiya mosque, the site of an even larger pro-Morsi sit-in.

"It was so quiet," remembered Dr Mostafa Hassanein, a young medic on overnight duty who walked back to Rabaa from the sit-in at around 3am to catch some sleep. "People were praying. The army was quiet too. Some of them were talking to protesters at the wire."

What happened next is highly disputed. But most witnesses agree an attack on the protest started shortly before 3.30am, as the worshippers knelt for the second and final time.

"At the second kneel of the prayers," said Moussa, in testimony corroborated by many others at the scene, "we could hear noises from the sides of the sit-in. So the imam interrupted his du'a [a religious invocation] and finished the prayers very quickly."

At either end of the demonstration, the watchmen manning the barricades had begun to clang together pieces of metal – an alarm used during the 2011 revolution to warn protesters of an imminent attack.

3.25am
Army on the move

Two hundred metres to the west, high up in a penthouse apartment, Seif Gamal woke to the cacophony. An engineer in his 40s who describes himself as unaffiliated to any political movement, Gamal and his family had been unnerved by the protesters' presence. Now he looked outside to see what was causing the alarm.

Advancing eastwards up Salah Salem Street, past the Mostafa mosque, were several armoured police vehicles, followed by armed men.

"Many armoured police vehicles were coming with many soldiers," said Gamal, whose name has been changed to avoid reprisals from state security. "They came slowly and stopped 100 metres short of the barricades before starting to shoot a lot of teargas – followed, around two minutes later, by a lot of firearms." Gamal said it was unclear at this stage whether the men were firing live rounds.

Realising the gravity of what he was witnessing, Gamal fetched a camera and began record the scene on video. The time on his watch, he said, was 3:26am. The footage was later uploaded by a friend to YouTube.

When it begins, the air is already thick with police teargas, and protesters can be seen gathering at the western barricade to see what is going on.

On the opposite side of the sit-in, protesters rising from dawn prayers were sprinting to the eastern barricades, near the Sayeda Safiya mosque – where a similar assault was taking place.

"When we finished the prayers, we rushed to the source[s] of the sound, because we thought it was thugs," said Dr Mohamedi. "But when we got there, we found it wasn't thugs but security forces shooting teargas. The teargas was coming from vehicles and soldiers were standing behind the vehicles. Then the soldiers started marching towards us firing."

Gamal had a clear view and was adamant that the attack was unprovoked. "I'm sure of that," said Gamal. "The police shot first. I didn't see any motorbikes, and I didn't hear any gunshots before." He added that sticks were the only weapons he had seen the protesters holding. "It was not a reaction to an attack. There was no attack from the demonstrators. They were praying. The police came slowly and surely towards the demonstrators. It was a plan."

Gamal's account is disputed by two residents who live further down the road.

Noha Asaad, cited in American media, said that security forces responded with gunfire after protesters guarding the western barricades used birdshot. Her neighbour Mirna el-Helbawy, a journalist who was also interviewed by many western outlets, agreed "it was obvious" that those in the sit-in fired first.

But it is unclear how either resident would have been able to see how the fighting started. The medics at the makeshift field hospital half a mile away in Rabaa al-Adawiya said the first dead body arrived there at around 3.45am. Yet Helbawy told the Guardian she may not have looked down from her balcony until as late as 3.46am, by which time – according to her own tweet (in Arabic) timestamped at 3.42am local time – firing had already started, calling into question whether she would have been able to work out who fired first. [The time on the tweet below will reflect your timezone]

Meanwhile, Asaad said she did not look outside before at least 3:55am, while her original witness statement on Facebook said the fighting started at 4.15am.

Ninety seconds into Gamal's video – by his reckoning at around 3:28am – one protester can certainly be seen firing what looks like a single-shot firearm towards security forces. But the soundtrack to the footage shows this is clearly not the first shot fired.

3.40am
Blood on the streets

Taha Hussein Khaled, an English teacher, had travelled down from Kafr el-Sheikh, an industrial city in the north, for the sit-in. When the clanging started, Khaled was one of the first to rush to the western edge of the site, fearing the protesters were under attack from anti-Morsi civilians. But reaching the barricade, Khaled realised the attackers were far more threatening: state security officials firing first teargas and then, he said, live ammunition.

"We stood our ground … [but] eventually the teargas became too much so we started to fall back," Khaled said. "I went through the bushes in the middle of the road to avoid being seen. And that's when I was shot. At 3.40am. I was running up Salah Salem Street, planning to turn right up Tayaran Street. Then I was shot through my left thigh."

A few metres behind him, Yehia Mahy Mahfouz, a teacher from Sohag, a small southern city, decided to hold his ground as police and soldiers advanced past the barricade. "As they [security officials] approached, I remained in place," Mahfouz said. "I wanted to tell them that there were women and children praying. Then a soldier hit me with his gun. I felt dizzy and then I fell on the ground. I was beaten on my jaw. Around nine soldiers surrounded me and beat me up with sticks."

In Gamal's video, one captured pro-Morsi protester can be seen being beaten by security officials.

Back at the centre of the sit-in, outside the club entrance, there was pandemonium. Parents scurried here and there, trying to find their children. Those who had been asleep emerged from their tents to hear Mohamed Wahdan, a senior Muslim Brother, shouting through the imam's microphone – calling on the soldiers to have mercy on a peaceful protest.

Nearby, from about 3.30am, 30 protesters including Dr Yehia Moussa formed a human chain along the barbed wire fence protecting the entrance to the Republican Guard club.

"We wanted to make sure that nobody threw any rocks or bottles to provoke them," said Moussa. "After about two or three minutes, the soldiers in front of the Republican Guard club started to put on their gas masks. Then two central security [riot police] vehicles came out of the Republican Guard building. They [the officers inside] were also wearing gas masks. They started to shoot teargas bombs to the far ends of the site first. And then they started to fire horizontally at human height level. Some people got hit [by the gas canisters]."

Ten minutes later, once the teargas became too much, many in the human chain sank to their knees. Moussa broke free, and tried to find something to soothe the stinging. On the other side of the junction, he found a bucket of water, which he used to wash his face and eyes. Then he tried to force his way back across the junction to the wire. But there was too much teargas, so Moussa took refuge instead behind the truck that had acted as a makeshift stage for the imam during dawn prayers.

To his right, coming from the eastern edge of the sit-in, he could see that at least one armoured police vehicle – followed by both police and army officers – had broken the sit-in's defences. Their colleagues approaching from the other end would not be far behind.

"I could hear and see them shooting live rounds," Moussa said. "They were already about 20 metres away."

According to those in the camp, the casualties now came thick and fast.

Mohamed Saber el-Sebaei said he had still been holding his prayer mat when he was hit.

"I was taking cover with another guy behind some rubble and I felt something hit my head," he said. "I held my prayer mat in my hand and I started to cover my head with it. But I couldn't stop the bleeding because there was so much blood."

Protester Mohamed Abdel Hafez – who was hit by a live round in his stomach – said he had been sleeping in his tent only minutes before becoming one of the first casualties. "I was asleep and woke up to the sound of shooting," he said later, in hospital. "I got up and I was shot."

Amid the chaos, at least 100 protesters fled into the nearest residential tower block, banging on any door they could find and asking for shelter and vinegar – a homemade remedy for teargas. The residents showed them up to the roof, where the police later arrested them. One petrified 11-year-old was still there by the afternoon.

Moussa was also one of the earliest casualties – hit by police birdshot on his left knee. He could stand the pain, just about, so he stayed at the truck until he was hit again two minutes later – by a live round just above his right knee.

The second injury was too much to bear, so Moussa turned and staggered for cover up Tayaran Street.

"It was there that I got my third injury. I felt a pain in my fingers. I looked at my hand and two-thirds of my right index finger had been shot off." Other protesters carried him to a nearby car, in which he was driven to the nearby Health Insurance hospital.

Hours later, while being transferred elsewhere, state television employees phoned him – as they often did after serious incidents – for a live interview on the casualty count. Moussa told them that he had been there himself, and that it was a massacre – before being cut off by the channel. Later in the day, he would be fired from his job as health ministry spokesman for spreading misinformation.

3.45am
First body in the field hospital

Up at the makeshift field hospital half a mile away in Rabaa al-Adawiya, Dr Alaa Mohamed Abu Zeid – the doctor responsible for recording the number of at the hospital – said casualties started arriving at around 3.45am. Days earlier, doctors had taken over a large room in the mosque compound, set up six beds, and filled several shelves with medicine – expecting to deal with simple maladies such as flu or heat stroke. They were not prepared for what happened that morning.

"The first case was a shot to the head," said Zeid, a radiologist who also volunteered at field hospitals during the 2011 revolution. "Part of the skull was missing, and the brain matter was seeping out." The man was dead.

Realising something serious was going on, the hospital manager woke all the doctors, and asked them to prepare for an emergency situation. But they could never have been ready for what happened next. There were only six beds, and in a worst-case scenario, doctors had expected to deal with just 25 cases at any one time.

"But this was a massacre," said Zeid. "We couldn't cope. All the time, we wondered when it would stop. But it didn't." By 4am, Zeid said there were already three dead people at the field hospital. Between 3.30am to 7.30am he claimed the hospital had received 12 dead bodies – often driven up Tayaran Street in private cars or motorcycles – and around 450 injured.

"Some people had bullets that came through both the back and the chest – which suggests they ran to one side, where they were shot, and then ran to the other side, where they were shot again," said Zeid.

Dr Mohamed Lotfy, in charge of the clinic's pharmacy, had also volunteered as a medic during the Libyan civil war. "It was the same kind of cases," he said, "as if we were in a war zone." Lotfy felt particularly emotional about it. While he may have been safe at the hospital, his mother, wife, two daughters and son were down at the Republican Guards' headquarters. "You can imagine how it feels to be running things over here," he said, "but to have your heart and mind over at the massacre."

By 4.30am, most of the clinic's medicine supplies had begun to run out. Those with minor were being sent to state and private hospitals in the area, where many complained of waiting hours to be treated – or even being turned away by officials frightened of involvement in a highly politicised situation. By 7am, Zeid recalled he had to roll up his trouser legs because there was so much blood on the floor.

"Regardless of how well-equipped a hospital was, no one would have been able to deal with what happened," said Zeid. "We were working and crying at the same time."

Zeid said the most heartbreaking cases included a 10-year-old boy, wounded by birdshot. A six-month-old baby was also brought in unconscious from the teargas, Zeid said – before being revived. While no child died during the incidents, these cases dispel the myth that the army and police did not harm women and children. Dr Khaled Abdel Latif, a surgeon working in the field that day, reported treating at least 20 women for teargas asphyxiation, while the Guardian met two women who were shot.

At one point, Dr Yasser Taha – Moussa's friend, and a well-known face to many of the doctors – was brought in on a stretcher, a bullet wound in his neck. "We couldn't believe it," said Zeid.

One of the doctors, Samer Abu Zeid – a heart specialist used to seeing blood in trauma situations – collapsed to the floor and broke down in tears.