The colonial authorities denied their request, and the Bakonjo and Baamba subsequently launched a low-intensity guerrilla war against the government in response.

[6][7] The violence reached its height in 1963 and 1964, when Tooro soldiers massacred Bakonjo and Baamba as they sought control over the lower valleys.

[8] After the Uganda–Tanzania War and the collapse of the regime of Idi Amin in 1979, Rwenzururian fighters looted abandoned weapons and supplies left by the retreating Uganda Army, reestablishing themselves as a serious threat in the region.

However in 1982, the administration of President Milton Obote negotiated a settlement with the leaders of the movement, in which they agreed to abandon the goal of secession in exchange for "a degree of local autonomy", the appointment of Bakonjo and Baamba to government administrative posts, and economic benefits such as vehicles and educational scholarships distributed by local elders.

[9] During the negotiations, the government preferred direct talks, as they believed third-party mediation would give legitimacy to the Rwenzururu claim.