The novel is set in the Dominican Republic, in both 1994—the “present day”—and during the period of Trujillo’s regime. In 1994, Dedé Mirabal lives in the house where her three sisters—Minerva, Patria and María Teresa—and her family used to live. Her dead sisters are known as the “butterflies,” they are martyrs and national heroes. In 1994, Dedé talks to an interviewer about her sisters’ lives and deaths. Her narrative is interspersed with her own memories of the past. The story’s point-of-view shifts between the four sisters from 1943 until the butterflies’ deaths in 1960. It encompasses Dedé’s memories, Minerva’s point-of-view, Patria’s point-of-view, and entries from María Teresa’s (Mate’s) diaries.

Minerva convinces Papá to allow the girls to go to a convent school, and there she meets Sinita, a girl whose male family members have all been killed by Trujillo. This is Minerva’s first insight into the devastating politics of the regime. Her next encounter with the dictator comes when she witnesses Trujillo seducing, and then abandoning, a friend of hers from school, Lina Lovatón.

Patria is the most religious of the sisters. As most people assume, she wants to become a nun. Patria soon discovers her sexuality, however, and gives up her dream of being a nun. Instead, she marries a farmer named Pedrito at age sixteen, and has a son, Nelson, and a daughter, Noris. When she delivers a stillborn child, her faith is shaken and she forsakes the church for a time. However, she later sees a vision of the Virgin Mary and her faith is restored. Throughout the novel, she is affected by a portrait of Trujillo that hangs beside one of Jesus, which to her represent God and the Devil, side by side.

Dedé becomes infatuated with Virgilio Morales, a young Communist intellectual who is always in trouble with the law, but Virgilio ends up dating Minerva instead. Dedé settles for marrying her cousin Jaimito, and Virgilio is eventually driven into exile by the Trujillo regime.

One day, Minerva discovers that Papá has a mistress and three illegitimate daughters. Amidst the chaos of this revelation, Papá gets invited to a party thrown by Trujillo. At the party, Trujillo tries to seduce Minerva. Minerva attempts to manipulate Trujillo into letting her go to law school instead. When he becomes vulgar, however, Minerva slaps him, and the Mirabals leave the party with dread hanging over their heads. The next day, Papá is arrested and taken in for questioning. Minerva is asked to have a “private conference” with Trujillo, but she refuses. She is questioned about her connection to Virgilio, and Papá is eventually released, though Minerva must meet Trujillo again for another weighted conversation.

Four years later, Papá dies, and Minerva goes to law school. There she meets Manolo, another revolutionary, and gets married. She graduates but, at the last minute, is denied her license by the government; she realizes that this is Trujillo’s revenge on her. Minerva and Manolo move in together, and María Teresa (who goes by “Mate”) stays with them. Mate becomes infatuated with a young man whose code name is Palomino, and who delivers weapons to Minerva. When Mate hears him refer to Minerva as “Mariposa” (Butterfly), and deliver guns, she realizes both his role and Minerva’s in the anti-Trujillo movement. Mate joins Minerva and Manolo’s secret resistance movement and marries Palomino, whose real name is Leandro.

Patria does not join the movement until her son Nelson decides to join Minerva’s revolutionaries. The church takes a neutral stance on Trujillo, but while on a religious retreat in the mountains, Patria sees Trujillo’s soldiers massacring some young revolutionaries. She is traumatized by this experience, especially as she sees a young man killed who is no older than her own daughter. Eventually, she and a young priest join Minerva’s underground group, together forming the “Fourteenth of June Movement.” Minerva, María Teresa, and Patria are now known as the “Butterflies.” The group uses Patria’s house to stockpile weapons.

The sisters ask Dedé to join their movement, but her courage fails her and she submits to Jaimito’s demand to refuse and stay far away from her troublesome sisters. Eventually, the SIM (Trujillo’s secret police force) arrest Pedrito, Nelson, Manolo, and Leandro, and then Minerva and Mate as well.

Patria stays at Mamá’s house during the arrests, and watches as the church finally speaks out against Trujillo. She eventually gets Trujillo to pardon Nelson. He offers Minerva and Mate a pardon as well, but they refuse. Minerva says that accepting a pardon would be an admission of guilt. Mate keeps a diary in prison; Minerva remains brave and strong but Mate starts to break down. The SIM torture Mate to get Leandro to talk. Eventually, the Organization of American States (OAS) comes to investigate the regime, and Mate is able to sneak them incriminating evidence which results in the sisters being released on house arrest.

By now, the “butterflies” are national symbols of the resistance. A friendly driver named Rufino takes them to visit their husbands in prison when need be. The men are moved to a remote prison in an attempt to force the sisters onto a desolate patch of land. On their fourth trip to see their husbands, the sisters are ambushed as they drive down a lonely mountain road. Minerva’s account ends at this point, but Dedé explains what happened afterwards. From accounts of various individuals, it is learned that the sisters and Rufino are killed and then put back into the car. The car is then pushed down a mountain so it looks like an accident. Everyone knows that Trujillo killed them, however, and they become martyrs.

In 1994, Dedé remembers Trujillo’s overthrow a year or so after the murder of her sisters, and the bloody revolutions that followed. She now lives with her niece, Minou, who is Minerva’s daughter. As the sole surviving sister, she has become a kind of “oracle” for the sisters, telling their story to the world and keeping their legacy alive.