Expansion beyond the territory of Buganda was what Lugard embarked on. He signed a treaty with the Omugabe of Ankole in the hope of blocking arms from reaching Bunyoro from the south and drove kabarega’s army which had occupied Toro out, and installed Kasagama an exiled Toro prince to the throne. Lugard then built a line of Forts along the southern boundary of Bunyoro a move which effectively stopped Kabarega from invading Toro, but not his deep dislike of foreigners and the British in this particular case. Kabarega not only welcomed elements opposed to Britirsh  rule into his kingdom, but enlisted their help and engaged the British severally in warfare until December of 1893 when Colonel Colville led a formidable force and confronted him but Kabarega burnt down his palace and fled to Bundongo forest where he continued his aggressions. However, he was eventually defeated and forced to flee to Acholi and Lango. Even  while there  he continued launching attacks albeit unsuccessful ones at the British who appended his Kingdom to the British protectorate on June 1896 and thereafter , a first formal agreement between Britain and Bunyoro followed in 1933.
Ankole kingdom fell more easily to the British for it had been weakened by smallpox, rinderpest, tetanus and jiggers in the 1870’s and early 1890’s which coupled with the tragic death of the Omugabe and all heirs to the throne in the epidemics, served Britain’s interests to well for they crowned a new young king who was the nephew to the late Omugabe Ntare. Consequently, Britain occupied the Ankole capital at Mbarara and met no resistance.
By the end of the 19th century, the Uganda protectorate formally included the kingdoms of Buganda, Toro, Bunyoro and Ankole.

British rule commenced in 1900 with the Sir Harry Johnston as the first governor. Britain ruled Uganda by using the Baganda as colonial agents, a reward for their collaboration with the administration and Buganda was the only Kingdom granted full federality, a privilege and status quo which elevated Buganda and Baganda above others and  he too expanded the protectorate further to incorporate more disparate cultural and linguistic  groups (none bantu) and to prevent unclaimed territories from being claimed by other European powers. Unlike other African countries like Kenya and to a lesser extent Tanzania which suffered white settlement, the colonial government discouraged white settlement in Uganda  and introduced cotton as a cash crop whose growing was left to the indigenous farmers unlike Kenya where tea was introduced but the indigenous people were not allowed to grow it but provide the labour needed to sustain production.

With cotton growing, the indigenous Ugandans sold their cotton themselves to co-operatives and were able to attain economic self sufficiency except the north which was neglected in terms of transport linkages to other parts of the country and in education