In 2000, the ALiR agreed to merge with the Hutu resistance movement based in Kinshasa into the new Democratic Forces for the Liberation of Rwanda (FDLR).

Following the invasion of Rwanda by the Rwandan Patriotic Front (RPF) led by Paul Kagame, many FAR and Interahamwe members fled across the border into Zaire.

The AFDL and their Rwandan and Ugandan allies forced the Hutu refugees back into Rwanda and scattering the ALiR fighters to countries such as Zambia, Angola, Congo-Brazzaville, the Central African Republic, Chad, Sudan, Burundi and Tanzania.

The ALiR's political wing, the Party for the Liberation of Rwanda (PALIR), maintained the old goal of overthrowing the Kagame government and regaining power, to which it added the objective of expelling the foreign invaders, thereby giving it more appeal to local populations.

In 1999, eight tourists from the U.S., United Kingdom and New Zealand and a Ugandan game warden were killed while in Uganda's Bwindi National Park, along the border with the DRC.

For the next several years, the battle lines stabilized and the war stagnated as Uganda and Rwanda competed to extract resources from the rich mines and forests of eastern Congo that they occupied.