(Bloomberg) — When disgruntled Sudanese spies took up arms and gunfire rang out across Khartoum, even members of the most powerful pro-government militia were startled.

As mutiny rocked three security buildings in the capital on Tuesday afternoon, fighters from the notorious Rapid Support Forces paramilitary group rushed to respond. By the next morning, five people — two of them soldiers — were dead, and the transitional government said the bloodshed sparked by a pay dispute was over.

But less than a year after President Omar al-Bashir was ousted in the wake of mass protests, the violence that left people cowering in the homes, canceled flights and temporarily cut oil production was a stark sign of the challenge still represented by elements of the Islamist leader’s 30-year regime.

As Sudan races toward what are supposed to be democratic elections in 2022. reforming the security sector is “a key fault line along which the transition could founder,” said Jonas Horner, an analyst with the Brussels-based International Crisis Group.

“These reforms require considerable political tact and deftness to avoid mobilizing a constituency still loyal to the ousted regime,” he said. “That constituency cannot be ignored or forgotten — after three decades in total control, they retain considerable power and hold over Sudanese politics and military.”

On paper, Africa’s third-largest country is edging toward democracy after the fall of Bashir, who swept to power in a 1989 coup and eventually turned the country into an Islamist-backed international pariah. Sudan now has a government of technocrats, including former United Nations economist Abdalla Hamdok as prime minister, an ex-World Bank official as finance minister, and experienced women in charge of justice and foreign affairs.

All the same, some key figures from the political-security alliances that helped sustain Bashir’s rule through years of economic devastation and regional rebellions have either retained many of their powers or may be lying low with plans to regroup. The United Arab Emirates and Saudi Arabia, which have typically acted to maintain the status quo, have pledged financial aid to the government.

The mutiny shows “the threat that Sudan’s sprawling military and security apparatus poses to the democratic transition,” said Jean-Baptiste Gallopin, an academic researching the country. “For democracy to take hold in Sudan, civilians will need to continue to disarm, demobilize or otherwise establish control” over all the groups, including the RSF.

The head of the RSF, Mohamed Hamdan ‘Hemedti,’ who once led brutal janjaweed militias in the western region of Darfur as Bashir’s enforcer, has pledged support for the revolution even after his fighters were accused of a crackdown in June that killed more than 100 protesters.

Late Tuesday, the militia leader who’s assumed a senior government rule and whose fighters often seem to wield more influence than the army, accused Salah Gosh, the ex-head of the now-restructured national intelligence service, of fomenting the unrest.

Abdel Fattah al-Burhan, the army chief who now heads the sovereign council that has quasi-presidential powers, also called the violence an attempt to abort the revolution and said 40 agents had been arrested. “The armed forces will remain cohesive to protect the transitional period,” he said.

Authorities said the mutiny originated in the Operations Unit, a paramilitary branch of the re-branded General Intelligence Directorate, among agents who chose not to be integrated into the RSF or military. A revolt also occurred in al-Obeid, a regional capital, while two southern oil fields were briefly shut down, removing 25,000 barrels per day, or at least a quarter, of Sudan’s output.

The head of the spy agency, Lieutenant General Abu Bakr Demblab, resigned after helping contain the incident and is being replaced, the General Intelligence Directorate said Thursday in a statement. About 5,800 of the agency’s roughly 11,700 staff have chosen to retire since Dec. 28 and are collecting financial compensation, it said.

The sovereign council said Gamal Abdul Magid, the head of military intelligence, would replace Demblab.

While the revolt was “poorly organized and seemed anarchic,” said Harry Verhoeven, author of ‘Water, Civilisation and Power in Sudan,’ “the unrest was a reflection of the deep divisions within the Sudanese security establishment and a logical outcome of the power struggles between Hemedti, Burhan’s army and the civilians around Hamdok that have been evident across Sudan.”

(Updates with resignation of intelligence chief in third-last paragraph)

–With assistance from Okech Francis.

To contact the reporters on this story: Mohammed Alamin in Khartoum at [email protected];Samuel Gebre in Abidjan at [email protected]

To contact the editors responsible for this story: Michael Gunn at [email protected], Karl Maier

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