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In 1884, Kabaka Mutesa died and his eighteen year old son Mwanga succeeded him. Kabaka Mwanga who distrusted the missionaries started persecuting the Christian leadership and demanded allegiance to the kingdom and traditional leaders. During the next several years, rivalries and armed conflict led to the ouster and reinstallation of Kabaka Mwanga three times as religious and political groups – British Protestants, French Catholics, Muslims loyal to Egypt, and German company agents east of the Buganda kingdom – armed or supported one kingdom and group over the other in pursuit of religious, economic and political dominance. By 1890, when Kabaka Mwanga was once again restored to power, he was little more than a figurehead for European interests. By this time, too, the kabakas were seen as instruments of the Catholic fathers, who represented French interests. This increased bitterness between Protestants and Catholics as the rivalries and hatreds of Europe were now played out on the African stage.

In 1884-85, Western European powers with designs on economic exploitation and increased global influence participated in the Berlin Conference which divided Africa into European colonies. England claimed what is now Uganda and Kenya but became alarmed over potential German influence within the Buganda kingdom when, in 1889, Kabaka Mwanga signed a friendship treaty with the Germans. The British and Germans signed an agreement in 1890, giving Britain full rights to Uganda while the Germans were given Heligoland, an island in the North Sea. Later that year, the British granted a charter and provided a military force to the Imperial British East Africa Company (IBEA) under the command of Captain Frederick Lugard which arrived in Uganda to consolidate Britain’s power and authority over Uganda both structurally and by force. By 1892, Lugard’s forces had defeated a final invasion of Muslim forces from Egypt, which had designs on establishing an empire in the region, defeated the French Catholic factions and reinstated Kabaka Mwanga to ceremonially head the Buganda Kingdom under British rule. Britain forced an agreement dividing the land up amongst religious/political factions, giving the Protestant (British) factions the most land and power, and the remainder to Catholic and Muslim groups. In 1894, Britain declared Uganda a “British Protectorate.”

There would be resistance movements thereafter, but always put down by the British or those whom the British now controlled. In 1900, weakened Buganda officials signed The Buganda Agreement with England, agreeing to subordinate all of their authority to the Protectorate. A new land tenure system was put in place, creating individual rather than kingdom allocated land. Hut taxes were imposed to force payment in British currency, destroying the bartering system and forcing cash payments to finance the Protectorate that was destroying indigenous values. Although the British had focused their attention on controlling the Buganda Kingdom first, they took control over all the kingdoms and clan led societies in present day Uganda, including Langi and Acholi by military conquest and the installation of puppet chiefs to employ British interests in Eastern Uganda. These compliant, Protestant puppet chiefs were given large tracts of land. They became landlords and charged exorbitant rent to those who had occupied their ancestral lands for generations. Some of the chiefs were deployed to impose British rule outside their own regions. Instead of fostering a common Ugandan identity, Britain accelerated divide and rule tactics, creating education systems which excluded Muslims and failed to develop a skilled or merchant class, favoring people from Buganda with civil service positions and forcing Acholi and Langi people into the army. The new religions became dividing lines which took on opposing political identities, further eroding cultural identities and the potential for unity. The British divided Uganda into tribal districts, ruled by a British colonial governor, with districts having no local political interaction. These well-conceived divide and rule strategies and tactics would prevent Ugandans from having a common national identity. Furthermore, an Asian merchant class from mostly India and Pakistan was invited to Uganda, became British citizens, acquired land and wealth and controlled much of the trade and business.

All in all, Britain ruled Uganda in ways to ensure the people would stay divided. It used violence to expand its territory outside the Buganda kingdom, especially in the North and East. This created anger against the people of Buganda, especially by the people in the north who saw Buganda as ruling them through Britain. Britain had also divided Uganda into economic zones, some regions designated for cash crops, others as reserves for cheap labor. Especially by excluding the civil service to all but people in Buganda, building an army of northerners, mostly Acholi and Langi, deciding who would be educated and who would not and building a merchant class among the Asian community, Britain created the foundation for a society in conflict with itself. Seeds of hatred and the quest for revenge were sown during the colonial era, and would continue after independence. People were divided along religious, ethnic, political, regional and class lines. The aim was to divide, so that Britain could rule. Britain’s ultimate aim was to control the trade and resources of its colonies and maintain political and military influence on a regional and global scale. Uganda, the colony was simply a means to an end and when independence would come, Uganda the nation would be too divided to unite.

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