The novel is set in the rural villages of the Igbo people of Nigeria during the 1920s and the story begins with a bitter feud between the villages of Umuaro and Okperi. The residents of Umuaro are at the brink of war with their neighbors in Okperi over a piece of disputed land. Nwaka, a man of considerable wealth and influence in Umuaro, pushes for the war against the advisement of Ezeulu, the Chief Priest of Ulu, ruling deity of Umuaro. In doing so, Nwaka audaciously defies Ulu, disregarding the deity and his chosen representative, Ezeulu, the only man who advises against engaging in tribal warfare.
The fight comes to a sudden halt through the involvement of an English colonial official, Capt. T.K. Winterbottom, who enforces the peace by destroying all the firearms within Umuaro. Winterbottom is compelled to side with Okperi after Ezeulu, resentful of his people’s heedlessness, testifies that Umuaro has no legitimate claim to the land. Despite the avoidance of bloodshed, some residents of Umuaro—including Nwaka—see Ezeulu’s testimony as a betrayal of his people.
A period of five relatively peaceful years passes, and a sense of normalcy returns to Umuaro. Christian missionaries have now made their way into Umuaro, converting whoever they can and convincing the people that the worship of their old gods is sinful and an exercise in futility. Seeing the faith of the white man slowly take root and gain ground in their community, Ezeulu sends one of his sons, Oduche, to learn as much as he can of the white man’s culture by having him attend a church that the missionaries have set up in Umuaro. Meanwhile, the enmity between Ezeulu and Nwaka has worsened and is now full-blown antagonism. Nwaka bolsters his position through his friendship with Ezidemili, high priest of the lesser god, Idemili, who has long been jealous of Ezeulu/Ulu’s reigning power.
Ezidemili’s ill will toward Ezeulu is worsened when Oduche—whom John Goodcountry has tasked with killing a totemic python, symbol of Idemili—locks the venerated serpent inside a box in a botched attempt to kill it outright. Any attempt to move or harm the holy snake is taken as a terrible insult to Idemili. When news of the violation reaches Ezidemili, he sends an envoy to Ezeulu to ask how he intends to make amends for his son’s crime. Ezeulu takes this questioning poorly and insults the high priest of Idemili in response.
While the tensions within the various Igbo factions continue to rise, Winterbottom prepares to carry out the British policy of indirect rule, which aims to appoint Africans as puppet leaders. T.K. Winterbottom sends emissaries to invite Ezeulu, whom he remembers favorably from the Okperi dispute, to Government Hill in order to name him “Paramount Chief.” Ezeulu refuses to comply and is eventually imprisoned for two months for his defiance.
Ezeulu rejects the new title, but Clarke, Assistant Deputy Officer to the now-ill Winterbottom, releases him nonetheless. Back in Umuaro, Ezeulu finally decides to take revenge on his people for their defiance five years ago and subsequent irreverence by refusing to initiate the New Yam Feast, the important harvest festival. He refuses to open the harvest because, due to his detention, he could not eat the ritual yams at two new moons and thus has two left over from the previous crop (the New Yam Feast can only be called when there are no yams left). Thus on Ulu’s authority, and exploiting this technicality, Ezeulu refuses the people their staple crop. The village elders even agree to accept Ulu's punishment if Ezeulu announces the harvest, but the Chief Priest rebuffs them.
News of the infighting attracts the attention of John Goodcountry, a Christian missionary, who sees the unrest as an opportunity to exploit in order to win more converts. The shrewd catechist announces that anyone who wishes to harvest his or her yams free of divine retribution has only to make an offering to the Christian God, instead of to Ulu.
The killing blow to Ezeulu/Ulu’s reputation comes with the tragic, untimely death of one of his sons, the strong, handsome Obika. The villagers take this turn of events as a sure sign that their god, Ulu, has abandoned his chosen cleric, undermining or possibly even destroying himself in the process. Rather than starve, the villagers flock to the church to make offerings to the Christian God.