The Walpurgis Royal Academy of Machinart was established in conjunction with the development of "Machinart," a type of magic that imbues mechanical dolls with life and intelligence, subsequently referred to as "automatons." Its objective is to train skilled puppeteers who can control these automatons, as militaries worldwide have begun integrating Machinart into their armies. Despite failing the academy's entrance exams, Raishin Akabane and his humanoid automaton Yaya must compete against one of the top one hundred students to gain entry to the Evening Party, a contest between puppeteers utilizing their automatons for supremacy. The victor is granted the title "Wiseman" and access to potent forbidden arts. Consequently, Raishin challenges Charlotte Belew and her automaton Sigmund to a duel; however, before they even commence, Sigmund is assaulted by other students. After saving his opponents from their attackers, Raishin cancels the duel but must subsequently search for an alternative approach to secure access to the Party. Driven by past tragedies, Raishin and Yaya collaborate to ascend to the top and claim the title of Wiseman.
Machine-Doll wa Kizutsukanai adapts the first three volumes of Reiji Kaitous light novel series of the same title.