The film tells the story of Ponyo, a goldfish who escapes from the ocean and is rescued by a five-year-old human boy, Sōsuke after she is washed ashore while trapped in a glass jar. As they bond with each other, the story deals with resolving Ponyo's desire to become a human girl, against the devastating circumstances brought about by her acquisition and use of magic.
Fujimoto, a once-human wizard, respects his daughter's choice, having decided he can trust Sōsuke. Ponyo then joyfully jumps high in the air and kisses Sōsuke, completing her transformation as a human.