Uganda

Inter-Christian insurgency between a cult army and the Ugandan government. Many atrocities and human rights violations.
 
Violent insurgency since 1987 in northern Uganda by a cult-like rebel group, the Lord’s Resistance Army (LRA) led by the mystic Joseph Kony. Ethnic undertones (particularly affecting the Acholi tribe and their fear of loss of influence in Uganda) and rivalry between different Christian religious groups (Uganda is a battleground between rival evangelical churches, fuelled by American sects).
 
2m people displaced, kidnappings, mutilation and thousands killed. Over 20,000 children have been abducted, to be used as soldiers, porters or sex slaves. 700,000 people still in protected camps, afraid to return home. The long conflict threatened to destabilise the central African region as rebels sought shelter in neighbouring countries and violence spilled over boundaries.
 
A landmark truce was brokered in August 2006 by Sudan, increasing stability in the war-weary north. A peace deal now has been made with the Museveni government of Uganda on the basis of local judicial traditions, but the situation is undermined by International Criminal Court war crimes warrants against LRA leaders (conflict of Western and African judicial systems). Violence also in the northeastern Karamoja region, where plenteous small arms encourage banditry and cattle raiding. Karamoja often suffers drought and food shortage.
 

Links:

Reuters Alertnet: Uganda
Wikipedia: LRA