With a fragile ceasefire barely inked, political and ethnic tensions running high, and tens of thousands of people sheltering in UN compounds across the country, the stakes for South Sudan could not be higher.

On the night of 15 December, a dispute between the country’s two leading military commanders-cum-politicians − President Salva Kiir and former Vice President Riek Machar − triggered armed conflict between pro-government troops in favour of Kiir on one side and opposition forces loyal to Machar on the other. The violence started in the capital Juba, but quickly spread to towns across eastern South Sudan.

The long-brewing tensions between the two men had peaked when Kiir dismissed his entire cabinet including Machar in July and in the lead-up to an overdue convention of the ruling Sudan People’s Liberation Movement (SPLM) in December.

Machar, who had declared his intention to run for president in 2015, and his allies (three of whom also said they would run) had been openly critical of Kiir’s chairmanship of the party, and more broadly of his increasingly repressive leadership. Hours after they boycotted the SPLM meeting, soldiers in the presidential guard − or so-called Tiger division − started shooting at each other in events that remain unclear.

Kiir is a member of the Dinka, South Sudan's biggest ethnic group, while Machar is a member of the Nuer, the country's second largest group, and when the fighting in Juba started, it quickly set off a domino effect of military defections by Nuer commanders and clashes between pro-government and rebel forces in several key towns.

On 16 December, Kiir accused Machar of having plotted a coup and detained eleven of his suspected allies, of whom seven have recently been released. On the streets of Juba, the violence took on dangerous ethnic overtones, with Dinka forces in the government openly targeting ethnic Nuer in neighbourhood round-ups and house-to-house searches, killing many in cold blood.

On my recent visit to South Sudan, a 34-year Nuer civil servant, wincing from his still raw gunshot wounds, claimed that on the afternoon of 16 December, Dinka government forces stopped him with his friends, took them to a building used by police and other forces in the Gudele suburb of Juba, locked them in a crowded room with around 200 others, and shot at all them through the windows.

“I was shot and lying on the floor,” he recalls, “people were lying on top of me.” He waited until evening then escaped into the night. Some other survivors were rescued the next day when other security forces arrived.

Civilians from both ethnic groups have been targeted in the fighting that has ensued. In Awerial county, I talked with some of the tens of thousands of Dinka families from the town of Bor who had fled attacks by rebel forces − including the fearsome White Army which currently supports Machar. People described narrow escapes as Nuer militants looted their livestock and destroyed their homes. Some said they saw dead bodies littering the streets. Thousands are still hiding in the toic, the flooded grasslands along the Nile.

Justice now

Over the last six weeks, the conflict has sowed distrust between Dinka and Nuer, polarised South Sudan’s political elite (although not necessarily along ethic lines), and wrought havoc on the communities of greater Upper Nile. Thousands of civilians have died, over 400,000 have fled their homes, and around 70,000 are now living in squalid conditions in UN compounds across the country.

The only silver lining is that it affords an opportunity for South Sudan’s leaders to break with the past – to “reboot” the government, as one parliament member put it in Juba. But regardless of the political solution forged at the peace talks under way in Addis Ababa, Ethiopia, there is a clear need to hold those resort to violence to account.

This is not something for which South Sudan has a good track record. There has been little or no justice for the many atrocities committed against civilians in the long civil war that eventually led to South Sudan’s creation. The 2005 peace agreement with Khartoum that ended the war had no provisions for holding people to account and kept leaders in place despite the blood on their hands. The post-independence government did not make justice a priority either, with the result that communities have continued to use violence with impunity, as in Jonglei State where attacks and counter-attacks have killed thousands.

The African Union’s (AU) decision to set up a commission of inquiry into the human rights abuses since the crisis started is a first step. If truly independent, impartial, properly mandated, staffed with experts, and well-resourced, it could prove highly important.

However, although the AU has participated in commissions of inquiry elsewhere, it has little experience running them. In South Sudan’s politically fractious environment with competing narratives of events, rigorous fact-finding and investigation is needed, not just to set the record straight but as a foundation for next steps. The interests of some African governments in the crisis also underscore the need for the commission to be properly insulated from AU politics.

Time is of the essence; with each passing day, communities become more polarised, evidence degrades, and memories blur. The AU should ensure the commission has a clear mandate to investigate alleged violations by both sides fully, identify those responsible, and make recommendations for holding them to account, including through criminal investigation and/or by making them ineligible for elections. The commission should welcome support from the UN, which has extensive experience and expertise in commissions of inquiry in crisis situations, and quickly make arrangements to preserve evidence already being collected by UN staff on the ground.

South Sudan’s leaders have a chance to turn a page in history, which takes courage and determination. They should reject any call for an amnesty and cooperate with all investigations – even if it means current leaders must submit to a process they can’t control.