After the war, some members of the group continued sporadic fighting in North Kivu as Armée Nationale Congolaise (ANC).
The RCD, operating in the east of the DRC, was a major factor in launching the Second Congo War (1998–2003), a rebellion against the government of Laurent-Désiré Kabila.
A split developed in the RCD between November 1998 and May 1999 as it became clear that some Rwanda-backed members based in Goma simply wanted to remove Kabila, rather than to introduce democracy.
Dr. Emile Ilunga was named leader of the mainstream Rwanda-backed faction known as the RCD-Goma from its base in the town of Goma.
RCD-Goma Chairman Adolphe Onusumba Yemba signed a peace pact in Sun City, South Africa, on 2 April 2003.
However Armée Nationale Congolaise (ANC) troops, the armed forces of the RCD-Goma, continued to occupy the city of Kanyabayonga along with local mostly Hutu militias created and directed by the North Kivu Governor Eugene Serufuli.
[9] In September 2003, the spokesman of the newly formed Transitional Government of the Democratic Republic of the Congo, Vital Kamerhe, accused members of the RCD-Goma of fomenting a new rebellion.
[11] On 10 and 11 October 2004, hundreds of mostly young students from primary and secondary schools took to the streets of the city of Kanyabayonga to protest against the increase in crimes against civilians by RCD-Goma forces.
In 2003, with the official end of that war, Nkunda joined the new integrated national army of the transitional government as a colonel and was promoted to general in 2004.
Azarias Ruberwa Manywa, secretary-general of the RCD-Goma, was named his movement's candidate for vice-president in a two-year national transition government.