Yoweri Museveni and Salva Kiir during the recent negotiations in Addis Ababa on South Sudan.

Within days of the outbreak of the violence in mid-December, the Uganda People’s Defence Force (UPDF) deployed to South Sudan at the government’s invitation. The UPDF’s mission at the outset was ostensibly to evacuate the over 200,000 stranded Ugandan nationals and to secure strategic installations in Juba. However, several weeks into the operation, President Yoweri Museveni disclosed that the UPDF was also involved in combat operations alongside government forces.

Indeed, the UPDF’s helicopter gunships, heavy artillery, tanks, and approximately 1,600 soldiers have been instrumental in helping the Sudan People’s Liberation Army (SPLA) retake cities held by anti-government forces affiliated with former Vice President Riek Machar. In a motion passed in the Ugandan parliament to retroactively approve UPDF operations, the UPDF’s raison d’íªtre in South Sudan was couched in terms of protecting the Ugandan expatriate community, ensuring Ugandan national security, and preventing genocide and other atrocities against humanity.

Nevertheless, the manner in which Uganda is securing its interests compromises concurrent efforts on the part of the Intergovernmental Authority on Development (IGAD), of which Uganda is a member, to mediate the crisis.

Although one of Machar’s “˜red-lines‘ prior to signing an IGAD-brokered Cessation of Hostilities had been the presence of the UPDF in South Sudan, he quickly exhausted any diplomatic or military leverage to strengthen his hand at the negotiating table. The Cessation of Hostilities signed last week between the Government of the Republic of South Sudan (represented by the Sudan People’s Liberation Movement/Army) and the Sudan People’s Liberation Movement/Army-in-Opposition stipulates that “armed groups and allied forces invited by either side” should be redeployed and/or progressively withdrawn. Yet, IGAD as a whole is yet to pressure Uganda to cease playing the diametrically opposed roles of combatant and peacemaker in South Sudan.

Museveni has long seen the stability of South Sudan as an important element of Uganda’s national security, and has demonstrated his willingness to intervene in South Sudan’s internal and external disputes. During a period of particularly heightened tensions between Sudan and South Sudan in April 2012, Museveni announced Uganda’s willingness to intervene on the part of the latter in the event of full-scale war. In addition, between 2010 and 2011, the late General George Athor led the South Sudan Democratic Movement/Army (SSDM/A), which was one of the strongest anti-government armed groups at the time. In December 2011, Museveni invited Athor to Uganda to participate in a confidential discussion of a Ugandan initiative to sponsor peace talks between the SSDM/A and the Government of South Sudan.

Days later, Athor was killed in an ambush with the SPLA in Central Equatoria, allegedly en route to recruit additional fighters in a part of South Sudan that was well outside his normal operating area of Jonglei. The SSDM/A and other anti-SPLA armed groups subsequently accused Museveni of having Athor assassinated in Kampala and staging his death by ambush in Equatoria. Coupled with his alleged complicity in Athor’s death, Museveni’s December 2013 threat that the nations of East Africa had agreed to go after Machar should he refuse to accept a ceasefire with the Government of South Sudan, demonstrates that Museveni’s interests are more aligned with maintaining the pre-crisis status quo than creating the space for a political settlement.

Museveni’s relationship with the SPLA spans four decades. During the civil war, Uganda not only provided financial and military assistance to the SPLA to fight the Government of Sudan, but the UPDF was even involved in direct combat operations in South Sudan. Museveni’s wartime support for the SPLA was especially critical between 1991 and 1993 – after the Ethiopian People’s Revolutionary Democratic Front (EPRDF) toppled the Derg regime, severed Ethiopian support for the SPLA, and expelled them from their rear bases. Furthermore, the additional setback posed by Machar’s attempt to unseat the late John Garang as head of the SPLA just months after the loss of the SPLA’s primary source of foreign support made Ugandan support during this time period vital.

In retribution for Uganda’s support for the SPLA, the Government of Sudan funneled support to the Lord’s Resistance Army (LRA) through Machar and other anti-SPLA groups to destabilize South Sudan and Uganda. When the Comprehensive Peace Agreement (CPA) was signed between Sudan and South Sudan, Machar, who had come back into the SPLA fold, was the lead negotiator for unsuccessful peace talks with the LRA. Due to the collapse of the peace talks in 2008 and Machar’s history of shifting loyalties, Museveni may be concerned that if Machar came to power in South Sudan, he could reignite his civil war-era relationships with Khartoum and the LRA to destabilize Uganda, despite the fact that the LRA is at its weakest point in years.

Aside from protecting Ugandans in South Sudan and ensuring Ugandan national security, Uganda also framed its intervention in terms of a need to prevent “genocidal and other atrocities against humanity.” Minister of Defence Crispus Kiyonga stated, “Africa must learn to defend itself. We saw what happened in Rwanda. Millions of people were killed as African states and [the] UN looked on. We must not allow a repeat.” As the international community prepares to commemorate the 20^th anniversary of the Rwandan genocide, such overt references seek to cast Uganda’s intervention in a moral, humanitarian light so as not to reveal Museveni’s actual realpolitik motivations. Yet, actions speak louder than words. By acting as a pro-government combatant rather than in a civilian protection capacity, Uganda has proved that its rationale of preventing genocide in South Sudan had no real merit.

Considering Uganda’s longstanding linkages to the current Government of South Sudan and Museveni’s professed anti-Machar sentiments, UPDF operations should have occurred under the auspices of IGAD, and with an African Union or United Nations mandate restricted to protecting civilians and strategic installations once its mission surpassed the evacuation of Ugandan nationals. Instead, Uganda’s current roles as both combatant and peace broker run the risk of damaging what is supposed to be a legitimate and nonpartisan IGAD mediation process.

Lesley Anne Warner is an Africa analyst at CNA’s Center for Strategic Studies and blogs on African politics and security at Lesley on Africa. Follow her on twitter  @lesley_warner