He worked closely with Tshekedi Khama, chief of the Bangwato tribe in the struggle to uphold tribal power over British colonial authority.

[4] As an opponent of Seretse Khama and his BDP), Bathoen signed, albeit reluctantly, an agreement for the drafting of a constitution and the independence of the protectorate of Bechuanaland from the United Kingdom in September 1966.

Unhappy with what he saw as an erosion of traditional tribal power in the country and the hasty democratization under Khama's rule, Bathoen abdicated his chiefship on 1 July 1969, after forty years of reign and ran as the presidential candidate for the BNF in the 1969 election.

For much of Bathoen's leadership, the opposition parties found themselves restricted to ethnic and regional strongholds, unable to establish a serious contest against the BDP.

[8] He remained critical of both the government and Koma's leadership of the BNF, encouraging the formation of the Botswana Freedom Party (BFP) in the late 1980s, although he did not lead it.