Prologue Set in the Zapata Swamp in Cuba, more than three decades before the main drama of Garcia's The Agüero Sisters unfolds, the prologue lets the reader in on the family secret that informs the main action of the novel. Ignacio and Blanca Agüero, husband-and-wife naturalists, are on the first collecting trip they've undertaken together in nine years. They're hunting ruddy ducks for a new museum collection in Boston. The trip takes on a slightly unreal aspect because of the unsparing sunlight: "On cloudless days like this, the light in the Zapata was so fierce that even the most experienced travelers were deceived, made to consider all manner of ruinous delusions.'' When Blanca spots a rare type of bee hummingbird, she turns to alert her husband only to find he's pointing a double-barreled gun at her. With no explanation, he shoots her and then carries her body seventeen miles to the nearest village, and lies about the deed.

Part I: Tropical Disturbances Garcia tells the intertwined stories of the Agüero family, and although each person's individual story is intricately connected to the stories of all the other characters, they are also essentially separate. This section opens with Reina Agüero climbing a telephone pole as she repairs a high-voltage cable outside El Cobre, a town in eastern Cuba. While fixing a water pump there, Reina is in a freak accident and is pinioned in the highest branches of a large tree that's hit by lightning. She receives skin grafts from loved ones and her scars become a symbol of family solidarity. Her daughter, Dulce, now has a missing strip of thigh and her scar "reminds Reina of the purplish burns on her own mother's forearms. Blanca Mestre Agüero had started as a chemist and bore the telltale signs of her profession's serious demands." After Reina recovers, she decides to visit Constancia in Miami and make peace with her own history.

Constancia is also undergoing changes. Her husband, Heberto Cruz, is determined to leave his successful tobacco business in New York and has purchased a condominium on Key Biscayne, Florida, where they'll retire together. Once the couple arrives in Florida, Heberto begins spending time with his brother, Gonzalo, and soon goes off on a counter-revolutionary mission, against Constancia's wishes. One night, Constancia dreams that her face is being operated upon by a plastic surgeon, and the next day she wakes to find that her face has been replaced by that of her mother. Around the same time, she goes into business for herself, marketing creams and lotions to women with a nostalgia for Cuba.

Interspersed throughout the present-day story are excerpts from Ignacio's diary. He tells of his own father, Reinaldo Agüero, whose job it was to read to the cigar workers in their factory, and of his own birth, which is brought on by his mother's sighting of a siguapa stygian owl, a bird that brings bad luck and that carries away his mother's placenta and rains blood on the town's parade. Constancia and Reina both muse on their pasts; when Constancia was a baby, her mother left home and returned years later nearly eight months pregnant. Although neither know that their father killed their mother, both are uncomfortable with the version of events they've been told.

Part II: A Common Affliction Ignacio's own story continues, with his being appointed a full professor of general science and biology at the University of Havana. He falls in love and marries the beautiful and mysterious Blanca Mestre.

Constancia's business, Cuerpo de Cuba, takes off, and she spends her days listening to...