Jiro, the son of a puppet maker named Hanji, is the main character of the novel. Due to difficult circumstances, he leaves his starving family and ventures out on his own. Jiro becomes an apprentice at the Hananza, a role that doesn't pay but provides him with food. There, he quickly forms a bond with Yoshida Kinshi, the son of the master puppeteer and a natural leader among the apprentices.

Kinshi is an intriguing character—stubborn, rebellious, idealistic, and willing to take risks. Initially, Jiro is just an average puppet painter, and Kinshi is not as skilled a puppeteer as his father would like. Despite this, Kinshi withstands his father's sarcastic remarks and physical mistreatment with a stoic resilience, reflecting both his samurai heritage and a deep, though concealed, respect for his father.

Jiro's parents, Hanji and Isako, are somewhat enigmatic figures, and their relationship is peculiar. At times, Hanji seems to be Jiro's ally and friend, while Isako often criticizes what she perceives as Jiro's clumsy and irresponsible actions. The presence of Jiro's parents is minimal throughout most of the novel, but they reappear in unexpected ways toward the end.

The Master Puppeteer features two other key characters: Yoshida, the current master puppeteer, and his former mentor, the now-blind story-chanter and playwright, Okada. Yoshida is a dominant force in the novel and in the lives of all the characters. He is brusque, arrogant, and controlling, yet surprisingly attuned to the needs and education of his apprentices, his audiences, and the impoverished people of Osaka. Though he criticizes his son Kinshi for poor performance, he secretly admires Kinshi's strength and ingenuity despite the harsh criticism. Yoshida restricts the apprentices from accessing the scripts needed to memorize puppet movements and stage directions, but he turns a blind eye when they steal them—similar to a Zen Buddhist teacher, he imposes limitations to foster the apprentices' resourcefulness.

Initially, Okada appears to be a minor character, akin to the wise old figures in Paterson's The Great Gilly Hopkins and Jacob Have I Loved. However, as the story unfolds, Okada's significance as the influential force behind the scenes—authoring and singing the stories for the puppeteers—grows, leading one to question if he is the true "master puppeteer" of the title. Throughout the novel, the enigmatic, Robin Hood-like bandit Saburo casts a shadow, continuing his audacious raids against merchants and authorities despite the hefty bounty on his head. Jiro frequently ponders Saburo's identity, whether he can be found, if he should be betrayed, and if Saburo would kill anyone who discovers his identity. These questions linger in Jiro's mind, adding a layer of intrigue to the story.

Recurring themes are prevalent in Paterson's works. A prominent theme is the father-son dynamic, especially evident in the relationships between Jiro, Kinshi, and their fathers. Both boys harbor valid suspicions or grievances against their fathers, yet the fathers strive to support their sons, albeit in unexpected and indirect ways.

Another theme Paterson explores is guilt, which is extensively examined after the pivotal chapter, "Command Performance." She delves into the broader issue of societal guilt—such as the guilt felt by those who have enough food towards those who are starving—and personal guilt. Paterson poses questions about Jiro's obligations to those who have aided him and whether he should feel indebted to those he has surpassed in his quest for success, particularly the other apprentices and his close friend Kinshi.

Paterson also explores the nature of art through her focus on puppet theater. A master puppeteer not only controls puppets but also influences the audience with the performances. Similarly, a master like...