After six years abroad, Khadija Saleh returned to Sudan in March to join protesters in the streets demanding change. She was taking part in a sit-in near the defence ministry in Khartoum on 3 June when security forces stormed in. The area had become a centre for anti-government protests.

The 41-year-old said she was beaten with sticks, and still wears bandages on her wounds. She explains: “I came back from a safer place because I want a better future for this country.”

Women were a driving force during months of protests against President Omar al-Bashir’s 30-year rule, before he was replaced by a military council in April. But the protests didn’t stop as demonstrators demanded the military swiftly hand power to civilians, leading to a stand-off and then a crackdown.

Nahid Gabralla, a 53-year-old activist, says she was beaten and threatened with rape during the raid. “Sudan can be better,” Gabralla says. “My daughter deserves to live in a nice country ... We will fight for a democratic Sudan, real change and for our rights.”

Physicians for Human Rights, a US-based group that investigates rights violations, cited local medics as saying women had their clothes torn off and were raped, but the extent of sexual violence was difficult to assess. Local women’s activists, citing multiple eyewitnesses, said soldiers held up women’s underwear on poles to symbolise those they had sexually assaulted.

“They know that if they humiliate the women, they will humiliate the whole people,” said 42-year-old activist Hadia Hasaballah. “None of the Sudanese women will officially say that they were raped because of the stigma.”

It was not possible to independently verify the reports of rape, and a spokesperson for the military council could not be reached for comment. The council has previously denied that rape took place. Sudan’s government-appointed Commission on Human Rights said it had launched an investigation into violations committed during and after the dispersal of the sit-in, which it condemned, without giving details.

Under Bashir’s rule, women’s lives were tightly controlled by men. Morality laws meant a woman could be arrested for wearing trousers. For that reason, 35-year-old Mahi Aba-Yazid wore trousers while she campaigned for change at the sit-in. She believes she was beaten more because of her choice of fashion. “There was already a bullet in my arm. I was bleeding but they continued to beat me,” she said.

The military council has said excesses were committed as the sit-in was cleared. It said these are being investigated and that those responsible will be held accountable. Despite the violence, Sudan’s military rulers and a coalition of opposition and protest groups agreed to share power for three years ahead of elections.

But Nagda Mansour, a 39-year-old translator who was imprisoned for 75 days after attending a demonstration in December, said it was difficult for many to accept the idea of negotiating with the military because of its leadership’s involvement in the war in Darfur. The Rapid Support Forces, headed by the deputy leader of the council, Mohamed Hamdan Dagalo, are accused of committing atrocities in Darfur. Officials in the past have denied those accusations.

The power-sharing agreement with the military council marks “the beginning, not the end”, says Mansour. “We as human rights defenders want to have a guarantee for transitional justice in Sudan,” she says.