Dubbed the "Justice First" marches, Saturday's demonstrations were called by the Sudanese Professionals' Association (SPA), which has been spearheading the protests since December that led to the military ousting of longtime leader Omar al-Bashir in April.
The marches mark 40 days since the dispersal of the pro-democracy protesters' sit-in in outside military headquarters in Khartoum on June 3. Thousands also turned out in Wad Madani, capital of Jazeera state, while others protested in Port Sudan, capital of Red Sea state, and Al-Ubayyid, capital of North Kordofan.
The deal, which also includes an FDFC-appointed cabinet, was meant to end a weekslong political deadlock between the military and protesters since the Khartoum sit-in site was cleared.
The agreement stipulates that the new governing body will be presided over by a military nominee for the first 21 months, and the last 18 months by a civilian.
"Blood for blood, even if (we get) civilian rule!" protesters chanted.
Waving a Sudanese flag, an 11-year-old boy said "all the mothers were crying in their homes when their children were killed".
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Several hundred also demonstrated in Khartoum's Burri neighbourhood, a working-class district and the cradle of numerous protests.
In Khartoum's twin city of Omdurman, hundreds demonstrated on al-Arbaeen Street, a major artery.
Many protesters were carrying banners that read "Justice for Martyrs", while others held photographs of demonstrators killed in the raid.
The protests in December swiftly escalated into nationwide demonstrations against the autocrat's ironfisted three-decade rule.
Protesters continued their sit-in, demanding that the generals themselves step down, ahead of the brutal dispersal on June 3.
The military council insists it did not order the raid, which according to the protest movement left more than 100 killed and hundreds wounded on that day.
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Sudan's ruling military council said it foiled an attempted military coup Thursday, just days after the military and a pro-democracy coalition agreed on a joint sovereign council to rule the country during a transition period until elections are held.
Omar said the alleged coup attempt was aimed at halting the power-sharing agreement between the TMC and the opposition Forces for Freedom and Change.
Intensive mediation of the African Union and Ethiopia led to a July 5 consensus on forming a "civilian and military" sovereign council to manage the country.
"We are in a real partnership".
Ibrahim said that the armed forces, rapid support forces, security, intelligence, and police will remain keen on the security and stability of the country and secure the gains and achieve the highest national goals and access to power through the ballot box, according to the Sudanese News Agency.
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