Khartoum, Sudan (CNN) In front of the military headquarters in Khartoum , workers are rebuilding the pavement. Men in khaki uniforms lounge under trees. Buildings here have been given a fresh lick of white paint, but the protest art and graffiti underneath is still faintly visible.

Authorities in the Sudanese capital are trying to erase any sign of the horrors of June 3, when troops, spearheaded by a paramilitary unit called the Rapid Support Forces (RSF), opened fire on a pro-democracy sit-in, killing at least 118 people , according to the Central Committee of Sudan Doctors.

Mu'men Ahmed, a 27-year-old leather bag and bracelet designer, was there that morning and filmed on his phone bullets raining down on the protesters.

"Snipers were targeting the people filming," he said. Ahmed explained he was shot in the hand and leg -- a bandage peaked out from the bottom of his shorts.

"I continued to film and then some shrapnel hit my head," he said.

The massacre that day horrified human rights activists and governments worldwide.

But perhaps it shouldn't have surprised them. The RSF is comprised largely of militias from the Janjaweed group, which became notorious for village-burning and rape during the Darfur conflict in west Sudan more than a decade ago.

After President Omar al-Bashir, who has been accused of war crimes for his role in Darfur, was removed in a military coup in April, a Transitional Military Council (TMC) took power, co-led by the RSF.

Their crackdown struck a fatal blow to hopes of a peaceful transition of power.

The similarity, albeit on a smaller scale, between what the Janjaweed did in Darfur and the RSF's actions on June 3 -- they allegedly burned protesters' tents, killed sit-in participants and, according to multiple accounts, raped female protesters -- did not escape Ahmed.

Rallying support

Muhammad Hamdan Daqlu -- more commonly known in Sudan as "Hemedti" -- is the Commander General of the RSF and was one of the leaders of the Janjaweed.

He is now the deputy head of the ruling TMC and has the biggest public profile of anyone in the military council.

Hemedti regularly addresses pro-RSF crowds, pushing the message that the men in uniform are trying to restore security and stability to the East African nation.

Earlier this week, hundreds of mostly male, tribal leaders packed a large, stuffy hall in Khartoum for a Hemedti rally. Many had traveled hundreds of kilometers from conservative areas of northern Sudan, which tend to side with whichever party is in power.

Sudanese soldiers guard a street in Khartoum on June 9, 2019.

Outside, a group of musicians banged on drums and blew horns, while men mostly in white robes and turbans danced, waving sticks or mobile phones. One man held a dagger in the air.

One speaker after another took to the stage to praise Hemedti, before -- after much applause -- he addressed the crowd and insisted that everything in the country was well. When Hemedti's microphone briefly stopped working, others on stage encouraged the throng to chant: "One people, one army. Unity is the choice of the people."

While Hemedti is not a particularly charismatic orator, the audience played its part, applauding in all the right places.

RSF troops tend to come from outside Khartoum, and many are from the Arab tribes in Darfur which fought on the side of the al-Bashir regime during the Darfur conflict. Consequently, many in Khartoum make a clear distinction between the Sudanese Army, which is seen as a national institution, and the RSF, which they view as a faction.

Hassan Jaafar, a tribal leader who attended the rally, said reports that Hemedti's troops had killed more than 100 protesters and raped dozens of women protesters were "not our business."

"We didn't see these things. It is not my business to go and investigate," he said. "But for me, I didn't see any killing or anything."

In another part of Khartoum, Sulaima Sharif, a native of the Sudanese capital who has been outspoken in her criticism of Hemedti and the RSF, said she knew of at least seven woman who were raped by RSF troops on June 3 -- and believes the number of rape victims is likely higher than that figure.

Sharif, who took part in the sit-in and runs a trauma center in Khartoum said the other women were probably too embarrassed and ashamed to come forward.

The targeting of female protesters was deliberate, said Sharif, who managed to escape unharmed. "They (women) have been beaten, threatened to be raped, being called sluts," she said. "This is too much!"

Sharif is seemingly not scared to speak out against the TMC. "Hemedti will kill us, all of us, anyway," she said. "If we stay home or if we go to the streets. At least we should die with dignity."

The TMC has denied committing rape on June 3.

End of a revolution?

Protests in Sudan began last year after an economic crisis led to high food prices and a shortage of cash. But they soon turned into an anti-Bashir movement.

After al-Bashir was removed in a coup in April, the protesters remained on the streets of Khartoum. The military council that assumed power had originally agreed on a three-year transition to democracy but talks broke down in May.

For the sit-in protesters, it was time to hand power back to the people with democratic elections.

People marching in Omdurman calling for the fall of the Transitional Military Council and chanting for civilian rule.

But since the June 3 massacre, people have been hesitant to resume protests in the capital, where the RSF has a heavy presence. The atmosphere in the city is calm but subdued, with fewer people venturing out in the evening, feeling that to do so could be unsafe.

Protest leaders have refused to restart talks with military leaders, who have been in damage control mode following international criticism of the attacks. They have said they'll investigate the crackdown but few in Khartoum have faith it will be fair.

The Sudanese Professionals Association (SPA), a body that led protests against former leader al-Bashir, has called for an independent committee to investigate the crackdown.

However, on Wednesday, in Omdurman -- Sudan's second-largest city which is located opposite to the capital across the River Nile -- the protest spirit lives on.

It started small. Just a handful of young men, and a few vocal pre-teens, chanting "freedom." As they walked down a dusty side street, women stepped out to join them. Within 100 meters, the crowd had tripled. Within 10 minutes, the march numbered over 100 people.

Protesters were banging pot lids and plastic buckets, chanting "madaniya, madaniya" -- short for "civilian rule" in Arabic.

"We want peace and freedom," said Manal, a doctor who did not want to use her full name and declined to say why.

For more than an hour, perhaps 200 people were marching in the dusty back streets, chanting, laughing, and chatting. The group planned to hold more, and larger, protests against the military council in the coming days, said one of the organizers, who asked not to be named for fear of repercussions from the RSF.

Sudan's revolution isn't over yet.