Mwanga II was the last monarch of an independent Buganda. He succeeded his father Mutesa I in 1884. Mwanga saw the greatest threat to his rule coming from the Christian missionaries that had gradually been penetrating the country. His father had tried to play-off Catholics against Protestants and thus balance the influence of the colonial powers that were backing each group. Mwanga took a much more aggressive approach expelling missionaries and insisting Christian converts abandon their faith on pain of torture or death. A number of young pages killed became known as the Ugandan Martyrs and were canonized in 1964. In 1885 he had the incoming archbishop James Hannington murdered on the border of his kingdom.

This raised the ire of the British, however, who backed a rebellion by Christian and Muslim groups that backed Mwanga's half brother and defeated Mwanga at Mengo in 1888. Mwanga's brother was elevated to the throne, but Mwanga escaped and negotiated with the British. In exchange for handing over some of his sovereignty to the British East Africa Company. The British changed their backing to Mwanga who swiftly deposed his usurping brother in 1889. In 1894 he accepted that Buganda would be a British protectorate.

He soon chaffed under British control and in 1897 revolted against the colonizers fleeing to the hills. On January 15, 1898 he was defeated at Kislaira by British backed forces. Captured he was in 1899 exiled to the Seychelles where he spent the rest of his life in exile. He was replaced on the Bugandan throne by his young son Daudi Chwa II .