A Colonel and the Question of Amnesty

At the age of 12, Thomas Kwoyelo was abducted by the Lord’s Resistance Army (LRA) while walking to his primary school in northern Uganda. During nearly twenty years in captivity, he participated in atrocious acts of violence. This included the abduction of children, rape, torture, and attacks deliberately targeting civilians. By the time Ugandan forces captured him in March 2009, Kwoyelo had risen to the rank of Colonel within the LRA hierarchy. Following his arrest, he publicly renounced the rebellion. Under the provisions of Uganda’s Amnesty Act of 2000, this declaration sparked debate over whether he qualified for amnesty despite his alleged involvement in serious crimes committed during the conflict.

Amnesty Disputes

With the Amnesty Act, Uganda installed an Amnesty Commission. It evaluates applications, determines eligibility, and issues certificates. However, under the Ugandan Constitution, the Director of Public Prosecutions (DPP) is vested with independent authority to block an amnesty if charges are filed against an applicant. While the Commission declared Kwoyelo qualified for amnesty, the DPP blocked his application. Kwoyelo would spend the next 15 years in pre-trial detention as his lawyers contested the state’s decision. In October 2025, he became the first person tried by Uganda’s International Crimes Division (ICD), established in 2008 as a domestic alternative to the International Criminal Court in The Hague. The ICD was created to prosecute war crimes and other serious offences. Kwoyelo was subsequently convicted of 44 counts of war crimes and sentenced to 40 years in prison. By then, more than 24,000 other former rebels, including commanders of higher rank, had received amnesty.

Two Visions of Justice

Uganda’s Amnesty Act offered former rebels reintegration instead of prosecution. Between 2000 and 2026, the Amnesty Commission granted 28,340 amnesties. Former LRA members received 13,605, or 48 percent of the total. These amnesties reflect a restorative approach to justice, which emphasizes healing and reintegration post-conflict. In northern Uganda, traditional rituals such as Mato Oput have served this purpose alongside the amnesty process. These rituals require offenders to publicly acknowledge their wrongdoing and seek forgiveness from victims. A different vision of justice emerged through criminal prosecution. They followed a retributive approach to justice. This focuses on holding individuals accountable through trials and imprisonment and became the mandate of the ICD.

A Hybrid System

Efforts to reconcile these competing approaches took shape during the Juba peace talks between the Ugandan government and the LRA. The June 2007 Agreement on Accountability and Reconciliation that resulted from these talks called for criminal prosecutions, traditional reconciliation, and amnesty to operate alongside one another. The agreement, however, did not specify when amnesty should take precedence over prosecution and peace fell through before full implementation. As a result, Uganda’s post-conflict justice system developed without a clear mechanism for deciding when reconciliation should outweigh punishment, or vice versa.

Legal Debates

Kwoyelo’s prosecution raised a fundamental question about the scope of Uganda’s Amnesty Act. In 2015, the Supreme Court of Uganda ruled that the DPP has unreviewable discretion to deny amnesty. The Court further held that crimes committed against civilians do not necessarily constitute acts carried out “in furtherance of war or rebellion” and therefore fall outside the protection of the Amnesty Act. It was also deemed to be “immaterial” whether other rebels in similar circumstances had received amnesty. This ruling allowed prosecutors to determine on their own which former combatants would face trial and which would be reintegrated.

Divergent Outcomes

No traditional ceremony as those mentioned earlier was conducted for Kwoyelo, and the ICD ordered no restorative, prescribing only retributive justice. Caesar Acellam, the LRA’s fourth-highest commander, experienced a very different process. He was described by Radhika Coomaraswamy, the then-Special Representative of the UN Secretary-General for Children and Armed Conflict, as “one of the worst perpetrators of child rights violations.” Witness accounts accused him of abducting children who were later forced into military service and slavery. Despite this, Acellam received amnesty and participated in a public ritual cleansing ceremony in northern Uganda’s city of Gulu in March 2015.

The Case of the Prosecution

The prosecution argued that Kwoyelo’s rank and conduct warranted retribution rather than amnesty. He held senior positions, including operations commander and director of military intelligence. Witnesses testified that he personally ordered massacres, including the killing of more than twenty women at the Pagak camp for internally displaced persons in May 2005. The DPP maintained that crimes of this gravity against civilians could not be forgiven under the Amnesty Act. From this perspective, Kwoyelo’s 40-year sentence reflected the severity of his actions.

The Case of the Defense

Critics of the ICD and the DPP do not necessarily dispute the gravity of the crimes attributed to Kwoyelo. Instead, they question why he was prosecuted while numerous other senior LRA figures received amnesty. Brigadier Kenneth Banya, a senior LRA commander captured by the Ugandan army in 2004, received amnesty. Brigadier Sam Kolo Otto, the former LRA spokesperson, also received amnesty. Several other LRA members who applied for amnesty were not prosecuted and instead joined the Ugandan army. Some have further argued that Kwoyelo’s prosecution was politically motivated, particularly because it was the first trial for the newly established ICD.

African Commission on Human and Peoples’ Rights

In 2018, the ACPHR concluded that Uganda had violated Kwoyelo’s rights under Articles 3 and 7 of the African Charter on Human and Peoples’ Rights. These articles guarantee equality before the law and the right to a fair trial. The Commission found that Uganda had denied him amnesty without providing a reasonable justification for treating him differently from similarly situated former combatants. The Commission noted that the Amnesty Act contained no explicit exception depending on the gravity refuting earlier DPP claims. The ruling did not suggest that serious crimes should be immune from prosecution. Instead, the Commission focused on the way Uganda applied its laws. If a state chooses to maintain an amnesty system, the Commission argued, it must apply that system consistently or clearly explain why certain individuals fall outside its protection. The Commission also encouraged Uganda to amend the Amnesty Act to exclude crimes of exceptional gravity from eligibility in future cases.

Tensions between Accountability and Reconciliation

The Kwoyelo case reveals a challenge that extends beyond Uganda. Hybrid justice systems that combine restorative and retributive methods without clear rules for choosing between them produce outcomes that can appear arbitrary, regardless of the merits of individual cases. For post-conflict societies seeking both accountability and reconciliation, the absence of such rules may risk undermining confidence in both tracks.