Songs of the Humpback Whale is the story of Jane Jones and her daughter Rebecca. Together they flee California and Jane's abusive husband, Oliver, a marine biologist who conducts research on humpback whales. They spend time on an orchard in Massachusetts where both women enter complex relationships with older men. Oliver tracks them down, Rebecca 's lover is killed in an accident, and the two women return home with Oliver.
Jane Jones, a speech pathologist, has been married to Oliver Jones for almost twenty years. Together, they have a teenage daughter named Rebecca. Oliver, a world-renowned marine biologist, has a history of being emotionally abusive and unavailable. After an argument that culminated in Jane slapping Oliver, Jane calls her brother, Joley, who is living and working on an apple orchard in Massachusetts. Through a series of letters, he guides her and Rebecca across the country until they are reunited, while Oliver begins tracking them down.
The orchard is owned by Sam, who employs and lodges his friend, Hadley, as well as Jane's brother, Joley. Soon, Jane and Sam begin an affair, and a relationship develops between Rebecca and Hadley. This is controversial, because Hadley is 25 and Rebecca is 15 (Jane is 35 and Sam is 25). Jane is worried about Rebecca and persuades Sam to chase Hadley away. Sam agrees reluctantly.
Eventually, Oliver is able to track Jane and Rebecca to the orchard. He arrives there with the intention of bringing them back to San Diego. However, Rebecca, afraid of being separated from Hadley, runs away to his mother's house where he is staying. They are discovered one morning on top of a mountain and confronted by Oliver, along with Sam and a park ranger. Hadley falls from the mountain to his death. Sick with pneumonia from spending the night outside, Rebecca has no choice but to return to the farm.
Confronted with the consequences of her actions, Jane returns home with Oliver and Rebecca.