Prologue
Set in Cuba's Zapata Swamp over thirty years before the main events of Garcia's The Agüero Sisters, the prologue reveals a family secret that drives the novel's central plot. Ignacio and Blanca Agüero, a married couple of naturalists, embark on their first joint expedition in nine years to collect specimens for a Boston museum. They're on the lookout for ruddy ducks. The trip feels surreal due to the harsh 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 bee hummingbird and turns to alert Ignacio, she finds him aiming a double-barreled gun at her. Without any explanation, he shoots her and then carries her body seventeen miles to the nearest village, fabricating a story about her death.

Part I: Tropical Disturbances
Garcia weaves together the interconnected stories of the Agüero family. Although each character's story is deeply linked to the others, they also stand alone. This section begins with Reina Agüero climbing a telephone pole to fix a high-voltage cable outside El Cobre, a town in eastern Cuba. During her work, Reina is caught in a freak accident, becoming trapped in the upper branches of a large tree struck by lightning. She receives skin grafts from family members, and her scars symbolize familial unity. Her daughter, Dulce, now has a scar where a strip of thigh skin was taken, which "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." Once Reina recovers, she decides to visit Constancia in Miami to reconcile with her past.

Constancia is also experiencing transformations. Her husband, Heberto Cruz, plans to leave his thriving tobacco business in New York and has bought a condo in Key Biscayne, Florida, for their retirement. After moving to Florida, Heberto starts spending time with his brother, Gonzalo, and soon embarks on a counter-revolutionary mission, against Constancia's wishes. One night, Constancia dreams of undergoing facial surgery, and the next morning, she wakes up to find her face has changed to resemble her mother's. Around this time, she starts her own business, selling creams and lotions to women longing for a connection to Cuba.

Throughout the current storyline, there are snippets from Ignacio's diary. He recounts his father, Reinaldo Agüero, who worked as a reader for cigar factory workers, and describes his own birth, which occurred after his mother saw a siguapa stygian owl. This ominous bird, believed to bring misfortune, carried away his mother's placenta and caused blood to rain on the town parade. Constancia and Reina reflect on their pasts; when Constancia was an infant, their mother left and returned years later, almost eight months pregnant. Although neither sister knows that their father murdered their mother, they both feel uneasy about the story they've been told.

Part II: A Common Affliction
Ignacio's narrative continues with his promotion to full professor of general science and biology at the University of Havana. He falls in love with and marries the enchanting and enigmatic Blanca Mestre.

Constancia's business, Cuerpo de Cuba, flourishes, and she spends her days listening to a radio show called "La Hora de los Milagros," or "The Miracle Hour." Her success is remarkable: "Each product in her Cuerpo de Cuba line will capture the elevated image Cuban women have of themselves: as passionate, self-sacrificing, and worthy of every luxury." Meanwhile, Heberto engages in his counter-revolutionary efforts in the Florida Everglades,...