The novel follows the protagonist, Onyesonwu (Igbo for "who fears death"), who is an Ewu, i.e. the child of an Okeke woman raped by a Nuru man. On reaching maturity, she goes on a quest to defeat her sorcerous father Daib using her magical powers. The novel is narrated by Onyesonwu to a journalist who interviews her before her execution. It is divided into three parts.
Part I
The novel opens with the death of Onyesonwu's Father, which occurs when Onyesonwu was sixteen. The plot shifts back to her arrival in Jwahir. Onyesonwu is a product of rape, her mother Najeeba's was raped alongside other Okeke women by a Nuru man when her village was attacked and destroyed by the Nurus.
Onyesonwu grows up in Jwahir after spending six years in the desert alone with her mother. She doesn't fit with the town people and is often ostracized because she is an Ewu. Onye meets a blacksmith named Fadil Ogundimu who treats her well, and eventually marries her mother. Onyesonwu undergoes female circumcision at eleven in an attempt to become normal and accepted by the community against her parents wishes, giving her biological father the chance to haunt her. She bonds closely with the three other girls who undergo the rites, Binta, Diti, and Luyu. Soon after the rite, an Ewu boy named Mwita arrives at school. Mwita and Onyesonwu befriends each other because of their shared status and shared powers, but Onyesonwu is skeptical about him because Mwita is trained by Aro, the local sorcerer, who refuses to coach her because she is a girl. After Onyesonwu father's burial Aro decides to coach her.
Part II
Onyesonwu's return to school days later after her father's death. She goes through a terrifying initiation which is literally her own death. She bonds with Mwita and develops her powers of shape shifting, resurrecting creatures, traveling to the ‘wilderness’ (spirit world) and she regrows her clitoris.
Onyesonwu's apprenticeship ends when she is mocked at the market and uses her abilities to make the mockers relive her mother's rape. After this, she leaves Jwahir and moves to help the Okeke in the west of the desert. Mwita, Binta, Diti, Luyu, and Diti's fiancé Fanasi decide to travel with her. On the way, Onyesonwu asks for direction to find the Nuru man prophesied by a Seer to rewrite the Great Book and she discovers that it was she who has been prophesied to rewrite the Great Book which justifies the oppression of the Okeke people and stop the Nuru attack in the west. The Seer was afraid to admit that an Ewu woman will change everything so he switched the race and gender.
Part III
Tension grows among the group due to the harshness of the desert and Luyu and Fanasi begin to have an affair after Onyesonwu regrows her friends clitoris despite Fanasi's betrothal to Diti. They reach a supply town where Onyesonwu and Mwita are stoned because of their Ewu status and Binta is killed in the process. Onyesonwu, out of rage, blinds everyone in the town. After Binta's death, they encounter the Vah, a tribe who travels in the sandstorm. The Vah invites the group to stay with them for the three weeks they plan on remaining there. Onyesonwu discusses with the goddess Ani and she meets a Kponyungo (dragon like creature) who takes her to the east. Onyesonwu's spirit travels to the west and attacks Diab but Diab uses an evil juju to poison her.
Diti and Fanasi return to Jwahir after the Vah sorcerers heal Onyesonwu and the others continue on their journey. Onyesonwu, Luyu and Mwita reach ruined Okeke villages and people and Onyesonwu heals the sick among them. They reach Durfa, where Onyesonwu attacks Diab and Mwita is killed by him. Onyesonwu uses her ability to move one of her eggs towards Mwita's sperm causing an explosion which injures Diab and eventually leads to his death.
Luyu and Onyesonwu discover that the blast killed all fertile men around the region and impregnated all the fertile women. They both flee to an island where Onyesonwu finds the Great Book. She rewrites it with a magical script called Nsibidi. The remaining Nuru men reach the island, kill Luyu and take Onyesonwu prisoner.
The epilogue, narrated by a Nuru who interviewed Onyesonwu, asserts that she was stoned to death and explains how he worked with his sister to dig her body. While a narration of the last two chapters by Sola describes Onyesonwu escaping execution by transforming into a Kponyungo and flying east to meet Mwita.
