We learn the events leading up to Sophia's Chrysalis.
"Would you say you are a happy child?"
Sophie, a young, bright, imaginative child, travels the world with her artist mother, author father, and brother Eric. Sitting in the embassy playing with another child, Sophie is quick to point out that his toy train has grown wings and can now go anywhere! The boy is stubborn, insisting that trains only run on tracks; Sophie tries to show him that there are also cities in the clouds, but the other boy is having none of it. Sophie is upset that other people can't see what she sees, including her friend, the toucan by her bedside. The toucan, Peeps, asks her about the cities in the sky, prompting her to keep dreaming.
Her father takes her outside to play, making sure to bring his ever-present jacket, which contains all "his wishes and his words". Her father mentions that long ago, a woman gave him all his wishes (candies that he keeps with him) because of a great deed he accomplished. Gerald is very distracted by his writing, and Sophie argues with her brother about what kind of wishes are valid: she believes that wishing for a million dollars is stupid, but can't name her wish right away. Her brother mocks her imagination, trying to destroy her beliefs with logic. "When it rains, all your cities in the sky get destroyed, don't they?" Sophie is upset, telling Peeps that he's the only one who likes spending time with her. She puts her father's wish inside a nearby tree: "I wish I could talk to you," she whispers as she runs off. Later on, she confides in Peeps that she thinks most people are sad because they can't see everything she sees, and she needs to show them.
At the Sydney Opera House, Sophie's father is preparing to present a selection of poems, and is therefore distracted from his daughter's imagination. At the beach after the fact, Sophie meets a woman with eyes just a bit like hers, who tells her that she has a secret name: Slink. Running off into the ocean to swim, Sophie discovers what she believes to be a merman under the waves. He presents her with a bubble that lets her breathe, and shows her the life under the ocean that lights up, and plays a song that only Sophie can here. The music seems to be only for her, and she does her best to remember it as it makes its way inside her mind via the bubble.
On the eve of the new Millennium, Sophie is in Burlington, Vermont, playing outside in the snow. Her brother is ill, and has been getting worse; he no longer even has the strength to stand on his own. Throwing snowballs back and forth, Sophie runs into a nearby copse of trees, meeting a woman crouched there. She asks if Sophie has any wishes left, and demands that she go and retrieve her father's coat, as she "needs her wishes and words back". She threatens to steal her father's ability to write away if Sophie doesn't do as she says, and then to cut open the girl's stomach if she doesn't obey. Sophie stands her ground as the woman draws a knife from her belt, telling her that her father only ever created two things, "one of which is now falling apart". She tells Sophie that there is ugliness everywhere in the world, and that her father, having worked for her for a decade now, wasted his talents on words and bratty kids.
Sophia forms a snowball in her hands, and tells the woman firmly that it is not snow, but fire, and that she better leave now, before it's too late. On the count of three, she launches the snowball, which ignites and explodes on contact with the woman, blazing light streaming out, and music playing in every corner of her mind. All of a sudden, all of Sophia's dreams make sense: the cities in the clouds, the trains with wings, Peeps, the underwater music, the wints. She watches the woman run away, terrified of the blazing apparition Sophia has become. She thanks the tree that has wrapped itself around her for its protection, and heads back to Eric, sitting alone on a bench.
Peeps tells her that their father chose to leave the world of dreams behind in order to raise them, and has ever since been trying to recapture it through his writing. Eric seems to see her differently now too, and tells her a secret: he now understands where their father's poem "Droplet" came from. Sophia begins to sing, trying to discover the words to the underwater song she heard so many years before.