"Unbreakable Machine Doll" is set in an alternate early 20th century where advanced technology has given rise to automatons, mechanical dolls powered by magical energy. The story centers on Raishin Akabane, a skilled puppeteer from Japan, who arrives at the prestigious Walpurgis Royal Academy of Machinart in England. His goal is to participate in the prestigious "Night Party," a brutal tournament where students and their automatons compete to become the ultimate puppeteer, known as the "Wiseman." Raishin seeks this title to exact revenge on those who destroyed his clan.

Raishin is accompanied by his automaton, Yaya, a highly advanced and sentient doll with a human-like appearance. Yaya is deeply devoted to Raishin, often expressing her affection in a playful yet possessive manner. Despite her emotional attachment, Yaya is a formidable combatant, capable of transforming into a powerful weapon. The duo faces numerous challenges as they navigate the dangerous and politically charged environment of the academy, where alliances are fragile, and betrayal is common.

Throughout the series, Raishin encounters other skilled puppeteers and their automatons, each with unique abilities and motivations. Among them is Charlotte Belew, a noblewoman with a strong sense of justice, and her automaton, Sigmund, a dragon-like creature. Another notable character is Felix Kingsfort, a cunning and ambitious student with a hidden agenda. The interactions between these characters reveal deeper layers of intrigue, as personal vendettas and political machinations intertwine with the tournament's stakes.

The narrative explores themes of revenge, loyalty, and the ethical implications of creating sentient machines. Raishin's journey is not only a quest for vengeance but also a path toward understanding the complexities of human emotions and relationships, particularly through his bond with Yaya. The series balances action-packed battles with moments of introspection, as characters grapple with their pasts and the consequences of their actions.

As the Night Party progresses, Raishin uncovers secrets about the academy, the true nature of the automatons, and the forces manipulating events behind the scenes. The story builds toward a climactic confrontation, where Raishin must confront his enemies and make difficult choices that will determine his future and the fate of those around him. The series concludes with unresolved threads, leaving room for further exploration of its richly constructed world.