Sailing from Lahaina, Maui to their homeport of Honolulu aboard their cargo-hauling schooner, Island Lady, Kaimana and his father, Slim, are attacked by a large humpback whale. She puts a hole in the bow of their ship, breaking several of the planks and damaging some of the ribs, causing water to pour into their small ship. Frantically, Slim and Kaimana make emergency repairs to save their vessel from sinking and taking them down with her. Once temporary repairs are made and they save their ship, they return to Lahaina for permanent repairs.

While in Lahaina repairing their ship, Kaimana feels the spirit of the whale calling him. This is 1856, and it has been reported the whale has a harpoon in her side, the unsuccessful attempt by whalers to take her. Kaimana knows he must go to her. After repairs to their ship, father, and son sail to where the whale had previously attacked them. There, Kaimana, the powerful son of his English father and Polynesian mother, sets out in their ship's dinghy to await the whale.

Eventually, the whale warily approaches Kaimana, her calf by her side, but not before he dreams of being a whale himself, one harpooned when coming to the water's surface for the precious air he needs to survive. Kaimana is successful in pulling the harpoon from her side, although he is wounded and barely able to stay afloat. Sensing his need, she lifts Kaimana to the surface like she would a newborn calf and nudges him back to his dinghy and survival.

She leaves him, but not before he can see that the sadness in her eyes has left, despite the pain. She knows she is going to live to take care of her calf.