In 2005 the Comprehensive Peace Agreement was signed by both NCA (National Congress Party) and the Sudan People’s Liberation Movement/Army (SPLM/A), ending the 12 year conflict over Southern Autonomy. Following this, a 6 year Interim period was underwent before South Sudan gained full autonomy where the NCP controlled Presidential, State, and local election processes as well as was assigned 15% representation in the First Southern Sudan Assembly while the the South received 85% representation in the legislature(2005). While this appears to be inherently equal, 70% of the total representation was designated for the SPLM party while the other 15% was divided among other Southern Political parties. This representation gap was due to 5 John Garang, co- founder of the Sudan People’s Liberation Army, becoming the Vice President of Sudan during the 6 Interim year period.
However 3 weeks into his term his helicopter crashed after a meeting with the Ugandan President Museveni to discuss upholding the Nairobi Agreement of 1999, to upgrade diplomatic status to ambassadorial, as well as to create a Joint Ministerial Committee to oversee cooperation, and is succeeded by Salva Kiir Mayardit. In 2005 a disarmament programme as apart of the CPA was implemented in Jonglei, in which the SPLA began with the Nuer cattle herders in Yuai, also known as the White Army. During the disarmament process, one of the South Sudanese soldiers reportedly raped a Nuer Women, starting a conflict that resulted in the beating of civilians, and the initial confiscation of 220 firearms. However as the forced disarmament of this ethnic group continued, more hostilities occurred as the Nuer needed their weapons for their migration to Ayod and Bur to protect their livestock from other ethnic groups in affiliated regions such as the Dinka and Merle, which resulted in the death of over 1,800 people. Similar conflicts arise in 2008 in the oil rich Abyei region however were state-backed as the South Sudan backed Dinka