(Bloomberg) -- As South Sudan’s main combatants prepare to join forces to end a brutal five-year civil war, recent fighting involving a renegade military officer suggests the conflict may be far from over.

Thousands of civilians have fled their homes in Yei state in the southwest of the country this year, witnesses to alleged murders, rape and looting as government troops battle an insurgency led by former Lieutenant-General Thomas Cirillo. Refusing to back a September peace deal signed by President Salva Kiir and main rebel chief Riek Machar, he accuses both of failing to address the personal and ethnic rivalries behind the war that’s claimed almost 400,000 lives.

That raises the prospect of more bloodshed in the oil-producing country that’s already suffered one of Africa’s deadliest conflicts this century and a litany of alleged war crimes. More than 4 million people -- a third of the population -- have fled their homes and there’s a persistent threat of mass hunger.

“A truce between Kiir and Machar is not sufficient to end all of South Sudan’s conflicts,” said Alan Boswell, a researcher with the Brussels-based International Crisis Group. While the size of Cirillo’s force is unclear, there’s a risk other, now quiescent, armed groups could follow his example if there are delays in implementing the peace plan.

Oil Jeopardy

There’s a threat for energy markets too. South Sudan’s oil -- sub-Saharan Africa’s third-largest in terms of reserves -- is concentrated in the northeast and was a target for Machar’s rebels during the conflict. Companies have restarted facilities in recent months, but planned increases in output depend on Kiir and Machar’s deal holding.

Already some of South Sudan’s factions are said to be recruiting more fighters -- including press-ganging children -- in case violence re-erupts.

The Crisis Group recently said there’s a high risk of the peace deal collapsing. The first major hurdle comes in May, when Kiir and Machar are due to form an expanded government. Before that, they need to agree on a unified national army and resolving disputes on local boundaries. Neither has been achieved.

A prior pact collapsed weeks into its enactment in July 2016, ushering in some of the war’s worst violence, including in Equatoria, which stretches from the capital, Juba, down to Uganda and was previously relatively peaceful.

A former deputy chief of staff, Cirillo was the highest-ranking Equatorial army official when he defected in early 2017. He’s since railed against strongmen from the Dinka and Nuer communities -- the largest of South Sudan’s about 60 ethnic groups, whose most prominent leaders are Kiir and Machar, respectively -- blaming them for fighting long-running power struggles.

Diplomatic Efforts

Cirillo told Bloomberg in 2017 that his National Salvation Front commanded at least 30,000 fighters from four rebel groups. He didn’t respond to recent requests for comment. Some of Cirillo’s representatives met March 14 with the Intergovernmental Authority on Development, a regional bloc that brokered the peace deal, to discuss his joining the pact. It didn’t mention any progress.

“We didn’t know that Salva Kiir and his cohort would turn completely evil against the people of South Sudan,” Cirillo told VICE News, the New York-based multimedia outlet, in February in a rare interview. He’s pushing for financial, legislative and judiciary powers to be distributed among the country’s states, counties and villages.

The fighting in central Equatoria in January and February sent 5,000 people fleeing into the northeastern Democratic Republic of Congo.

Equatorians “have felt occupied for years, both by government forces and cattle-keeping militias,” said Boswell. “These sentiments have only grown more intense since the deployment of and abuse by government soldiers from Kiir’s ethnic group since 2016.”

©2019 Bloomberg L.P.