The narrative is set on the island of Cuba in 1550, and with the incidents said to have been taken from West Indian legend. Act One sees the narrative set on a plantation on the coast of Cuba. Isidora, a woman over whose birth hangs a mystery, is in love with Felix. Her adopted father, Patronio, would prefer that she marry a Count, but unbeknownst to all the Count has drowned and is being impersonated. Meanwhile Felix attempts to locate a buried treasure so that he can marry Isidora when the Black Rover appears and kidnaps the lovers and the fake count, Henry T Smith, along with a group of Patronio's slaves.
Act Two, set on board the pirate's ship, sees the prisoners condemned to death, but they are saved by Isidora when she sings a song that was sung to her by a woman, perhaps her mother, when she was a babe. The pirate's anger is dampened, and soon after the prisoner's escape on a raft, leaving the pirate ship to sink.
In the final act Isidora and her fellow captives return to the plantation to find happiness, except for Smith, who is gaoled. The opera also contains several sub-plots and intrigues concerning mistaken identity, lust and love, human sacrifice and a curse.