The novel takes place in the Dominican Republic, both in 1994 and under the Trujillo regime. In 1994, Dedé Mirabal lives in the house where her three sisters used to live. The dead sisters are known as the “butterflies,” and they are martyrs and national heroes. In 1994 Dedé talks to an interviewer about her sisters, and her narrative is interrupted with memories.
The story shifts between the four sisters from 1943 to their deaths in 1960: Dedé’s memories, Minerva’s point of view, Patria’s point of view, and entries from María Teresa’s diaries. Minerva convinces Papá to allow them to go to a Catholic school, and there she meets Sinita, a girl whose family was killed by Trujillo. Minerva watches Trujillo seduce and abandon a girl at her school, Lina Lovatón.
Patria is the most religious sister, and she wants to become a nun until she discovers her own sexuality. She marries a farmer named Pedrito at age sixteen, and has a son Nelson and a daughter Noris, but her next baby is stillborn. This shakes her faith, and she is especially affected by a portrait of Trujillo located next to one of Jesus.
Dedé becomes infatuated with Virgilio Morales, a young Communist intellectual, but Virgilio and Minerva end up dating instead. Dedé settles for marrying her cousin Jaimito, and Virgilio is driven by the Trujillo regime into exile.
One day Minerva discovers that Papá has a mistress and three illegitimate daughters. Papá gets invited to a party thrown by Trujillo, and there Trujillo tries to seduce Minerva, while she tries manipulate him into letting her go to law school. She slaps him, and the Mirabals leave. The next day Papá is arrested and taken in for questioning. Minerva is asked to have a “private conference” with Trujillo, but she refuses. Papá is eventually released, and Minerva meets Trujillo again for another battle of wills.
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—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 who delivers weapons to Minerva, whom he calls by her name in the anti-Trujillo movement: “Mariposa” (Butterfly). Mate joins Minerva and Manolo’s secret resistance movement and marries the young man, whose name is Leandro.
Patria remains uninvolved until her son Nelson wants to join Minerva’s revolutionaries. The church is neutral regarding Trujillo, but while on a religious retreat in the mountains Patria sees Trujillo’s soldiers massacring some young revolutionaries. She is traumatized by this, and she and her 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 demands that she refuse. Then 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, and watches as the church finally speaks out against Trujillo. She eventually gets Trujillo to pardon Nelson. He offers Minerva and Mate a pardon, but they refuse. Mate keeps a diary from prison, where Minerva remains brave and strong but Mate starts to break down. The SIM torture Mate to get Leandro to talk. The Organization of American States comes to investigate the regime, and the sisters are released into 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. On their fourth trip, the sisters are ambushed as they drive down a lonely mountain road. Minerva’s account ends, but Dedé explains what happened – the sisters and Rufino are each killed and then put back into their car, 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 the Mirabals, and the bloody revolutions that followed. She now lives with her niece Minou, Minerva’s daughter, and has become a kind of “oracle” for the sisters, telling their story to the world.