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The primary theme of A Grain of Wheat is the importance of national independence. A corollary is the difficulty of achieving independence because the colonial system prevented colonized subjects from gaining the necessary skills of self-governance. Closely related to these themes is the personal abuse of power among both colonizers and the colonized. Along with this theme goes the harm caused specifically by hypocrisy and, more generally, the selfish misuse of political stance for personal purposes.

Although Ngugi wa Thiong'o provides substantial material on the causes that Mau Mau arose and the workings of the larger Kenyan independence movement, his novel is not primarily a social and political analysis. Rather, he focuses on the human elements in the late colonial era and the related efforts to free Kenya’s diverse peoples from British rule. He shows how the variety of social conditioning in which diverse characters were raised later influenced their attitudes toward independence. Personal decisions based on emotion play central roles, especially among people who sought to distance themselves from political commitments. The author shows that no one is truly immune from the legacy of colonialism. At the same time, he seems not to place full confidence in those who espouse political and altruistic motives for their actions.

The characters of Mugo, who accidentally becomes a hero, and Gikonyo show how ordinary people can get caught up in something larger than themselves; one becomes a traitor, and the other is broken by his experiences. The falsity of Karanja by betraying all his people is paralleled by his personal behavior in his sexual relationship with Mumbi to betray her husband. The deep longings of Wambui and Warui to see freedom in their lifetimes are apparently achieved, and their subsequent disappointment at the limits of social change in the new nation encapsulate common frustrations.