In a nondescript apartment block in downtown Khartoum, 14-year-old Faisal Ali rests with his father. In the entrance hall, the strong traditional smell of Sudanese brides’ perfume still lingers. Before last month’s brutal crackdown, the building was home to young newlyweds and visitors to the capital.

Today, it is a safe house for protesters, including children, who face life-changing injuries.

Faisal, from Kutom in North Darfur, lost his leg after he was shot at multiple times by Sudan’s National Intelligence and Security Service. “He is a child. He doesn’t know much about politics,” his father said.

On the day the former dictator Omar al-Bashir fell in April, Faisal had been at a school for Qur’an studies, where his father had sent him to improve his Arabic. Everyone in his village had begun running towards the security service building. “I was running with other people when a man in a military uniform shot me three times,” Faisal said.

Unable to get proper medical treatment in Kutom, he was referred to Fashir, the capital of North Darfur, only to find there was no surgeon there. When he arrived in Khartoum he was told his leg must be amputated.

The location of the safe house is kept secret to protect protesters and the activists who help them. One of the injured protesters was shot in the back in early June, when security forces fired at a mass sit-in, killing 128 people. It is feared he is still wanted by the authorities. Two of the activists helping at the safe house were themselves injured during protests on Sunday. One was shot in the stomach and another beaten with sticks.

On Tuesday, the Sudanese Professionals’ Association, which has spearheaded the protests demanding civilian rule, said two of its leaders had been arrested. Separately, the bodies of four protesters, thought to be organisers at neighbourhood level, were found in Omdurman. Neighbourhood committee members are the backbone of the uprising in the country, and without them protesters fear it will be even harder to organise.

Protests against Bashir, Sudan’s long-time dictator, began in Atbara in December. Since the military removed him in April it has refused to permit civilian rule.

On Friday protest leaders struck a deal with the ruling generals on a new governing body. The deal provides for the interim governing body to have a rotating presidency, as a compromise between the positions of the generals and the protesters.

People celebrate in Khartoum after Sudan’s military leaders and opposition groups struck a deal. Photograph: Mohamed Nureldin Abdallah/Reuters

On Sunday, tens of thousands of people took part in further protests across the country – the first large-scale demonstrations since the deadly crackdown on a protest camp in June.

Faisal is staying in the safe house with five other injured people – some are protesters, others were caught in the crossfire. The house was set up by an unnamed group of volunteers in April, when Bashir fell, and is funded by the Sudanese diaspora in the Gulf countries, Europe, Canada and the US. Donations cover the rent for each flat – 500 Sudanese pounds (£9) a day – and a daily allowance of 550 Sudanese pounds for each person.

“We also send money to the rest of their families in Darfur,” said Mohamed Saad, a volunteer with the group coordinating the safe house.

Ahmed Yassen, 16, from Zalinji in Central Darfur state, has also lost a leg. Like Faisal, he came to Khartoum with his father.

The day Ahmed arrived in Khartoum, his mother, who is living with the rest of their family in a camp in their town, gave birth. The volunteer group sent money for his mother to buy milk for the baby. “When she heard that doctors had cut the leg off her son, her breasts stopped giving milk. She is in shock,” Ahmed’s father said.

Ahmed wasn’t protesting when he was shot. He had just left work at a cafe when he saw crowds chanting and moving towards him. “Then people in plain clothes opened windows and shot me and so many others,” he said.

The security services have continued to crack down on people known to have taken part in protests. Several employees at the ministry of oil and gas and the Family Bank in Khartoum were arrested after they participated in recent sit-ins.

One woman, who was detained for five hours at the national security offices in Khartoum, told the Guardian she had seen six other people who belonged to different ministries also being held.

Women from the ministry of health have complained about being verbally sexually harassed by soldiers from the feared Rapid Support Forces (RSF), a paramilitary force that was heavily armed by Bashir. The forces were deployed at their offices after the dispersal of the sit-in, and were withdrawn only two days ago.

“I stopped parking my car outside the ministry for fear of getting harassed by the RSF. I now park it inside the building just to avoid them,” said one woman, who is a doctor.

The RSF soldiers have been accused of raping dozens of protesters, including two female doctors, when they dispersed the sit-in in June.

• Names have been changed to protect the identities of the protesters.