In rural Kenya, two Gikuyu villages called Makuyu and Kameno sit on two ridges, divided by the Honia river. The villages are rivals and often antagonistic toward each other, but they are united by their dependence on the same river for water and agriculture.
Chege, an elder of Kameno, believes that his son, Waiyaki, is the prophesied savior who will rescue their people from the invading white colonialists. Although Waiyaki is still a boy, all can see from a young age that he is a natural leader with an unusual sense of power in his eyes. Chege believes that Waiyaki must understand the white people if he is to defeat them, so he sends his son to study at the school in the nearby town, Siriana, under a white missionary named Reverend Livingstone. Waiyaki’s friends Kamau and Kinuthia accompany him, and they study there for several years.
Joshua, a Gikuyu Christian pastor from Makuyu, has two daughters, Nyambura and Muthoni. A devout Christian, Joshua strictly forbids his daughters to be circumcised, as is the custom of Gikuyu women, believing that it symbolizes the tribe’s evil ways. However, although she loves Christianity, Muthoni decides that she wants to be circumcised so that she can be a “real woman” in the tradition of their Gikuyu ancestors. Although Joshua threatens to disown her, Muthoni defies him and gets circumcised (on the same day that Waiyaki is circumcised and thus becomes a man). Muthoni feels complete and no longer in conflict with her identity, but her circumcision wound grows infected. Waiyaki takes her to the mission hospital in Siriana, but she dies while she is there.
Muthoni’s death deepens the divisions between the two villages. Makuyu, where Joshua lives, becomes devoted to the white people’s Christianity, even as Kabonyi—Kamau’s father and Joshua’s disciple—abandons the faith and becomes a fierce opponent of it. Kameno becomes committed to protecting the tribe’s traditions and purity from the white colonists’ corruption. The mission school reacts by banning all children whose parents practice Gikuyu customs, which includes Kinuthia, Kamau, and Waiyaki. The villagers hear news that white settlers across the country are exiling Gikuyu people off of their lands or forcing them to work as serfs. They fear that the white people will disrupt their agrarian way of life.
Banned from the mission school, the three young men build their own school in Kameno to spread education to the Gikuyu in the ridges. Although Kabonyi believes they must fight the encroaching white people with weapons, Waiyaki believes that only education can help them fight the white people and their new governments. He wants to unite Makuyu and Kameno under the cause of educating their children in order to fight together for their political freedom. The villagers and even people from surrounding ridges herald Waiyaki as their new leader and savior, naming him the Teacher.
However, Kabonyi envies Waiyaki’s popularity and believes that he should be the tribe’s savior instead. He starts sowing dissent against Waiyaki and scheming to destroy him. As part of this plan, Kabonyi forms the Kiama, a governing council meant to protect the tribe from Joshua and his white people’s religion. Although Waiyaki wants to simply focus on education, the tribe elects him to the Kiama and forces him to take an oath that he will protect the tribe’s purity and customs.
Although Kinuthia tries to warn Waiyaki that Kabonyi and Kamau conspire against him, Waiyaki is too absorbed in his own goals to pay any heed. However, he fails to call for unity between the Christians and the Kiama when he has the chance, because he is afraid that such a call would risk his popularity and influence among the villagers.
Waiyaki and Nyambura meet and fall in love with each other, even though such a relationship is forbidden both by Joshua, since Waiyaki works with the Kiama (though he is also a Christian, he is not devout) and by the Kiama, since Nyambura is uncircumcised and thus not a true woman of the tribe. Waiyaki asks Nyambura to marry him, and though she loves him, she refuses because she fears her father’s wrath. However, Kamau and Kabonyi learn of Waiyaki’s proposal and use it to turn the people against Waiyaki, since he has broken the Kiama’s oath of purity. In the end, Waiyaki tries to call for unity and education so that together their people can resist the white colonialists and vie for their political freedom. However, Kabonyi challenges Waiyaki, claims that he himself is the tribe’s savior, and reveals Waiyaki’s love for Nyambura. The tribe demands that Waiyaki denounce his love for Nyambura for the sake of the oath. When he refuses, they turn on him and give him and Nyambura over to the Kiama for judgment and punishment.
The villagers are ultimately ashamed that they so readily sacrificed their own savior. The hills return to silence and to sleep, unable to rise against the white colonialists who invade, take lands, and demand taxes.