South Sudan’s quiet reversal

South Sudan entered 2025 under the appearance of political continuity, but with the atmosphere of a country holding its breath. At the center of that tension was Riek Machar, the First Vice President and long-standing rival to President Salva Kiir, whose return to government under the 2018 Revitalized Peace Agreement had been framed as the final act of a civil war that refused to end cleanly. More than seven years later, that agreement remained intact on paper and increasingly irrelevant in practice.

In February 2025, violence involving the White Army, a network of armed Nuer youth militias, flared in Upper Nile. Clashes erupted in Nasir County. By early March, those clashes had escalated into full-scale conflict, leaving dozens dead, tens of thousands displaced, and a United Nations helicopter crew member killed. Markets were attacked, communities emptied, and families fled into swamps and neighboring counties, uncertain whether return was possible or even desirable. The violence did not erupt suddenly, it followed months of smaller confrontations and retaliations, a slow-motion unraveling of trust within the political class.

The government accused Machar of backing the group and of treason, allegations his party denied, and swiftly removed him from his post. He was placed under house arrest in Juba. Senior figures within the Sudan People’s Liberation Movement–In Opposition (SPLM-IO) were detained, including military commanders, cabinet ministers, members of parliament, and party officials. Some were released without explanation. Others were not. The arrests signaled that the trial was only one element of a broader campaign to neutralize Machar’s political base.

Soon after, legal proceedings were initiated against him, reopening a case that many South Sudanese and international observers regard as procedurally flawed and politically foreclosed. The court, critics argue, answers to the same executive authority that stands to benefit most from Machar’s conviction, collapsing the distinction between accuser, arbiter, and enforcer. Recent reports have further complicated the situation. According to leaked diplomatic communications, the South Sudanese government requested U.S. support for the prosecution of Riek Machar after agreeing to accept U.S. deportees. While this does not legally determine the outcome of the trial, it has reinforced public perceptions that the government is politically committed to securing a conviction rather than allowing an independent judicial process. For many citizens and SPLM-IO supporters, this development deepens doubts about the neutrality and credibility of the proceedings.

As the case moved forward in fits and starts — hearings postponed, resumed, and suspended again — the political environment deteriorated. Across the country, governors appointed under the peace deal were removed and replaced with figures loyal to the ruling SPLM-IG. In Upper Nile, Jonglei, and the Equatorias, the opposition’s administrative presence was dismantled with little pretense of legality.

The political rupture soon found expression on the battlefield. By December, fighting had intensified in Jonglei State, where ethnic composition, geography, and the legacy of wartime mobilization made the region particularly combustible. Jonglei is home to large Lou Nuer populations and has long been associated with the White Army, whose fighters are drawn less from formal command structures than from communal networks, predominantly within Lou Nuer communities. As government forces advanced, civilians were ordered to evacuate entire areas deemed hostile. The distinction between militia and population, already thin, collapsed altogether.

The crisis in Nasir, and the subsequent wave of arrests and the trial itself, revealed what the prosecution of Riek Machar had only hinted at: that South Sudan’s postwar settlement had failed not through dramatic collapse, but through steady erosion. Legal institutions functioned without credibility. Military operations blurred into collective punishment. And a peace agreement designed to end a civil war became, instead, a framework through which its conflicts were managed, postponed, and ultimately resume.

Historical context

South Sudan’s independence in 2011 was the endpoint of a war that had shaped nearly every aspect of its political and social life. For decades, southern insurgents fought successive governments in Khartoum — first from 1955 to 1972, then again from 1983 to 2005 — in what became one of the longest-running conflicts on the African continent. The 2005 Comprehensive Peace Agreement, signed in Naivasha by John Garang of the Sudan People’s Liberation Movement and President Omar al-Bashir, ended open warfare and created the conditions for a referendum on secession. Millions of South Sudanese who had spent years displaced inside Sudan or living in refugee camps across East Africa saw independence as a moral reckoning for that history.

But the new state inherited the habits of a liberation movement rather than the institutions of a government.

Barely two years after independence, political tensions inside the SPLM hardened into open rivalry. Disputes between President Salva Kiir and senior party figures, most prominently Vice President Riek Machar, polarized the leadership ahead of anticipated national elections. In July 2013, Kiir dismissed Machar and dissolved the entire cabinet. Machar denounced the move as authoritarian, and the political system, already thin, began to buckle.

That rupture was followed by a sweeping purge of the military and security services. Deputy chiefs of staff were removed, dozens of major generals dismissed, and more than a hundred senior officers forced into retirement. These decisions fractured trust within both the SPLM and the national army, transforming political disagreement into existential suspicion.

On 15 December 2013, the government accused Machar and his allies of attempting a coup, an allegation he denied. Fighting broke out within the Presidential Guard in Juba and quickly spread beyond barracks and checkpoints. The violence assumed an ethnic character almost immediately. Nuer civilians were targeted in the capital, marking a decisive turn from elite power struggle to mass conflict.

From Juba, the war expanded into the Greater Upper Nile region — Unity, Jonglei, and Upper Nile states — areas with large Nuer populations and longstanding grievances against the central government. Towns such as Bor, Malakal, and Nasir became battlegrounds. Additional armed actors entered the conflict, including the Agwelek militia led by Gen. Johnson Olony, who initially fought alongside government forces in Upper Nile as part of informal security arrangements.

Over time, the war’s logic changed. What began as a confrontation between rival political leaders increasingly fractured along communal lines. In Upper Nile, fighting between Agwelek forces and White Army militias aligned with Machar came to be framed locally as Shilluk versus Nuer. Political objectives blurred into ethnic narratives, and violence became both more localized and more difficult to contain.

Mass atrocities followed. In Malakal and surrounding areas, civilians were killed, women raped, children abducted, and entire neighborhoods erased. By the end of the first phase of the war, roughly eight hundred thousand people had fled to Sudan, while hundreds of thousands more were displaced internally or scattered across neighboring countries. The violence entrenched cycles of retaliation and permanently altered South Sudan’s social fabric.

The outbreak of civil war exposed the structural weakness of South Sudan’s post-independence order. The SPLM, having transitioned from a guerrilla movement to a ruling party, proved unable to manage internal competition through institutional and democratic means. The party fragmented into rival factions, setting the stage for prolonged instability rather than consolidation.

The peace agreements

Years of fighting hollowed out the state. The economy collapsed, the currency lost value, and public employment — particularly in Upper Nile — disappeared. Large segments of the population sought refuge in UNMISS Protection of Civilians sites, where temporary shelter became semi-permanent residence.

In 2015, the first Agreement on the Resolution of the Conflict in South Sudan was signed. It did not hold. Renewed fighting erupted in Juba in 2016, forcing Machar to flee the country once again. Political volatility deepened in 2017 when the army chief of staff, Paul Malong Awan, was dismissed and placed under house arrest. After his release, Malong went into exile and, in early 2018, announced a new rebellion.

A second attempt at peace followed. The Revitalized Agreement on the Resolution of the Conflict in the Republic of South Sudan was signed in September 2018 in Addis Ababa. It promised a unified army, a permanent ceasefire, and a transitional government leading to elections. Much of it remained aspirational. Forces were never fully integrated. Key institutions were delayed or abandoned. Violence continued in multiple states.

Fragmentation at the political center persisted. In 2019, Pagan Amum, a veteran SPLM figure, broke away to form the Real SPLM. In 2024, Kenya hosted the Tumaini initiative in an effort to bring non-signatory opposition groups into a broader settlement. It produced little.

In Equatoria, government forces remained locked in battle with the National Salvation Front. In Jonglei and the Greater Pibor Administrative Area, violence among Nuer, Dinka, and Murle communities continued largely untouched by national peace deals. In Warrap, Lakes, and Unity states, clashes between Dinka sub-clans and neighboring groups produced thousands of civilian casualties each year. Since 2020, more than three thousand civilians have been killed annually in these conflicts alone.

The humanitarian impact

The cumulative effect of these wars has been a sustained humanitarian crisis. Renewed violence in Jonglei and Western Equatoria displaced tens of thousands, pushing communities into neighboring states and already fragile regions. Government figures estimate that more than two hundred thousand people have been newly displaced, most from Jonglei.

The government has defended its operations. Ateny Wek Ateny, the minister of information, described military action in northern Jonglei as lawful and necessary to restore order and protect civilians. Opposition groups insist they are acting in self-defense. Regional and international actors — including IGAD, the African Union, and the European Union — have warned that the fighting threatens the future of the peace process, concerns heightened by statements attributed to Johnson Olony urging forces to “spare no one.”

The deeper problem predates the current crisis. The SPLM was never unified around a governing ideology capable of holding a state together. That coherence existed largely in the person of John Garang. After his death, political loyalty increasingly followed ethnic lines. Tribe came before nation. The party fractured easily; conflict ignited readily. Recovery has proven elusive. The country continues to grapple with overlapping layers of strain — political paralysis, unresolved historical grievances, recurring humanitarian emergencies, and severe economic breakdown — each reinforcing the other and pushing millions into ever more precarious living conditions. And until that hierarchy is reversed, peace in South Sudan is likely to remain provisional.