Despite instability, political progress continued. In May 2005, a new constitution was adopted by the national assembly, and overwhelmingly ratified in Jan. 2006. On July 30, 2006, the first democratic election in the country since 1970 took place. President Kabila received 44.8% of the vote, which was not enough to win the election outright. Fighting broke out between factions supporting the two major candidates, setting off the worst violence the country has seen since the 2002 peace deal was signed. Kabila was declared the winner in the October run-off election, winning 58% of the vote, the countrys first freely elected president in four decades.

In August 2007, a rebel general, Laurent Nkunda, led battles between his militia, made up of fellow Tutsis, and the Congolese Army. The fighting continued throughout the year, driving hundreds of thousands of people from their homes in eastern Congo and threatening to spiral the already fragile country back into civil war. Nkunda claimed he was protecting Tutsis from extremist Rwandan Hutus. In January 2008, the government and the rebels signed an agreement that had both sides withdrawing their troops and the rebels disarming and eventually being integrated into the national army. The cease-fire fell apart in August, and fighting resumed between Nkundas militia and the army. By the end of October 2008, the rebels had captured the major army base of Rumangaboebel and were advancing towad Goma, the capital of North Kivu province. In addition, angry civilians attacked UN peacekeeping troops, who proved ineffectual in both thwarting the rebels and protecting citizens. Nkunda was arrested in January 2009, and a cease-fire was signed on March 23, 2009. Members of Nkundas militia joined the government forces. The militaries of Congo and Rwanda worked together to eliminate remaining rebel fighters from eastern Congo. The joint mission lasts about five weeks.

A report released in January 2008 by the International Rescue Committee found that despite billions in aid, the