Arrow of God is set in rural Nigeria during the 1920s in a southern part of the country where the Igbo people reside. The novel begins with a war between two neighboring regions of rural Igboland: Umuaro and Okperi. Though we don't know the boundaries of Okperi, we do know that Umuaro is made up of six villages. These six villages are linked by their worship of a common god, Ulu.
The people of Umuaro start a war with Okperi over land they want to claim; they are encouraged to start the war by a wealthy man named Nwaka, who challenges Ulu. This war is launched against the advice of Ulu's chief priest, Ezeulu. The colonial administration steps in to stop the war and rules in favor of Okperi after discussing the matter with Ezeulu, the one man in Umuaro who tells the truth. Captain Winterbottom, a British colonial official who commands the local station, breaks and burns all the guns in Umuaro, becoming a legend. Meanwhile, the people of Umuaro become angry with Ezeulu because he didn't take their side.
Five years later, life in Umuaro has returned to normal. Sort of. Christian missionaries have made major inroads into society, establishing converts and trying to show that the old gods are ineffective. Ezeulu is sending his son Oduche to church, to be his eyes and ears, and to learn the ways of the white man. Animosity between Ezeulu and Nwaka and their respective villages has grown to the point called kill and take the head (4.1). In other words, things have gotten to the point where men in the two villages try to kill each other using poison. Nwaka is fortified and strengthened by his relationship with Ezidemili, the high priest of the god, Idemili. Though Idemili is a lesser god in comparison to Ulu, the competition between the two priests is dividing Umuaro, creating suspicion and ill will among brothers.
But the competition isn't limited to within the Igbo religion; the missionaries call the Chrisitan Igbo, including Oduche, to kill the sacred python. Oduche chickens out at the last minute, putting the snake in a box instead, but his family discovers the terrible deed when he's at church. Doing anything to the royal python is considered an abomination. The royal python belongs to the god Idemili, and as soon as the priest of Idemili hears about it, he sends a messenger to chide Ezeulu, and to ask what he intends to do to purify his house, (i.e., to make up for what his son tried to do). Ezeulu responds by telling Ezidemili to die (literally) and the matter rests there, uneasily.
The colonial administration has commissioned a new road to be built, connecting Okperi with Umuaro. They've run out of funds, but still need to complete the road, so Mr. Wright, the overseer, petitions to conscript labor. He receives permission and Umuaro is the unlucky recipient of the demand for free labor. One day, Ezeulu's son Obika is late getting to work. He had too much palm wine to drink the day before. But when Mr. Wright whips him, it stirs up the resentments of all the men. Why are they forced to work for free, when Okperi men are paid for their labor? What makes them different? Why should they be treated like this? Though they grumble among themselves, they are never able to come to a decision about what to do.
Because Ezeulu assumes that Obika has done something to deserve the whipping, he precipitates a crisis in his own household. Edogo, his oldest son, gets to thinking, and decides that the old man's propensity to choose favorites among his sons has created a problem. He believes that Ezeulu has tried to influence Ulu's decision about which son will be the next priest. By sending Oduche to learn the religion of the white man, Ezeulu has essentially taken Oduche out of the running. And Ezeulu has trained Nwafo in the ways of the priesthood, so he's clearly staking his claim on Nwafo as the one Ulu will choose. But Edogo begins to wonder what will happen if Ulu doesn't choose Nwafo, if he chooses Edogo or Obika. It will create conflict and division in the family and Edogo, as eldest son, will have to deal with it. He goes to Ezeulu's friend, Akuebue, and asks him to speak to Ezeulu.
Akuebue finds that Ezeulu is not receptive to a talk about the divisions within Umuaro, blaming the people of Umuaro for the white man's arrival. The people of Umuaro try to blame Ezeulu because he told the white man the truth when Winterbottom stepped in to stop the war between Okperi and Umuaro.
Ezeulu is also unreceptive to reports of divisions within his own household. He admits that he sacrificed Oduche, not so much to put him out of the running for the priesthood, but because he sees the threat to Umuaro and to the Igbo posed by Christianity. Such a situation requires the supreme sacrifice, that of a human being.
Meanwhile, Captain Winterbottom has been under another kind of stress. "Indirect rule" is the ideology that rules the day and he is under direct orders to find a chief for Umuaro. He decides that Ezeulu is just the man for the job, and sends a messenger to fetch Ezeulu. Ezeulu refuses to come, saying that the Priest of Ulu doesn't leave his hut, and dispatches the messenger back to Winterbottom with the message that if he wants to see Ezeulu, he'll have to come visit Ezeulu. Winterbottom issues an order for Ezeulu's arrest and sends two policemen to fetch him.
The next day, after consulting with the elders and men of title in Umuaro, Ezeulu decides to set out for Okperi, to find out what Winterbottom wanted. His heart is angry because Umuaro continues to blame him for the white man's presence, and because they don't show Ulu proper respect. His archenemy, Nwaka, continues to challenge Ulu and the people do nothing about it. The two policemen sent to arrest Ezeulu pass him on the way, but don't realize it until they reach his compound and learn that Ezeulu has gone to Okperi.
In Okperi, Winterbottom suddenly becomes ill. The African servants decide that Ezeulu must have a lot of power because Winterbottom is struck ill only after he issues the warrant for Ezeulu's arrest. So when Ezeulu arrives, the servants are afraid. They don't want to lock him up as ordered; instead, they pretend that the guardroom is a guest room and try to make him comfortable.
On this first night in Okperi, Ezeulu has a vision and realizes that his real battle is with his own people, not with the white man at all. In his vision, he sees Nwaka challenge Ulu, and the people spitting on him (Ezeulu), saying he is the priest of a dead god. He begins to see that the white man has been able to take advantage of Umuaro's division to sow further seeds of destruction. He hopes Winterbottom detains him for a long time, so he can better plan his revenge.
Ezeulu is detained for a couple of months. First, Clarke decides to teach him a lesson by making him wait. Then he offers Ezeulu the position of chief, but Ezeulu refuses. Angry, Clarke claps him in prison, and Winterbottom commends him, saying he should keep Ezeulu locked up until he learns to cooperate. But Clarke begins to suffer pangs of conscience, realizing that he doesn't have a legitimate reason to keep Ezeulu imprisoned. He's relieved when he hears from Winterbottom's superior advising against creating new Warrant Chiefs. This gives Clarke the excuse to let Ezeulu go.
Ezeulu returns home. Everybody is glad to see him again and Ezeulu realizes that his anger was directed not against his real neighbors but against an idea that they were mocking Ulu and disrespecting Ezeulu. Nevertheless, he lays low and sets his plan in action. When the time for announcing the Feast of the New Yam comes, he fails to announce it. His assistants come to ask if he's forgotten his duties. He gets mad and sends them away.
Next, the elders of the village come and ask, gingerly, why he hasn't announced the Feast of the New Yam. Ezeulu tells them that he has three sacred yams left. He can't announce the Feast of the New Yam until he has finished all the sacred yams. He was unable to eat the sacred yams while imprisoned in Okperi, and now he has to follow the rules – one yam a month. The men are horrified. If they wait three months before they are allowed to harvest their crops, the crops will be ruined and the people of Umuaro will suffer widespread famine.
The elders tell Ezeulu that he should just quickly eat the yams and if there are any repercussions, they will ask Ulu to let it descend on their heads, not Ezeulu's. But Ezeulu is steadfast. Such a thing is unheard of. And anyway, no matter what their intentions are, as chief priest he will be the one to suffer the consequences of breaking the rules. He can't do it. They must wait.
The Christian catechist, Mr. Goodcountry, recognizes this as an opportunity. He says that anybody who wants to offer their yams to the Christian god instead, so they can harvest their yams, will receive the protection of the Christian god as well. As people begin to suffer, they do just that. Meanwhile, Obika – who is sick – is asked to help in the funeral preparations for Amalu, one of the elders in the village who had died some months back. He helps with one of the funeral rituals by carrying the mask for Ogbazulobodo, the night spirit, and chasing after day. He runs so hard and so fast, however, that he drops dead when he returns.
The people say it is a judgment against Ezeulu. His god, Ulu, has spoken: Ezeulu has become stubborn and proud, and the god has not sided with his priest against the people. But it was a bad time to humiliate the priest. It allowed the people to take "liberties." That year, many of the yams were harvested in the name of the Christian god; and the crops reaped afterwards were also reaped in the name of the Christian god. As Arrow of God comes to a close, it seems that worship of the Christian god has replaced that of Ulu.