In 1863, Kyoto stands at a crossroads. The final years of the Edo period have brought political upheaval, rising tensions, and bloodshed to the streets of Japan's capital as the nation grapples with the arrival of foreign powers and the decline of the shogunate's authority. It is in this turbulent atmosphere that a young orphan named Nio Chirinu works at his adoptive grandmother's dumpling shop, dreaming of a better world while carrying a burning sense of justice within him.

Nio's life changes forever when he crosses paths with Toshizo Hijikata and Soji Okita, two members of a feared and despised group of masterless ronin known as the Miburo. Short for Mibu Roshigumi, this collection of rogue samurai patrols Kyoto's dangerous streets using ruthless methods. After Hijikata and Okita use Nio and his sister Iroha as bait to capture child abductors, they recognize the boy's pure-hearted determination and invite him to join their ranks. Despite his inability to wield a blade effectively, Nio accepts, hoping to understand how to truly change the world and protect the innocent.

Nio joins alongside two other young members of his age: Hajime Saito, a skilled left-handed swordsman carrying the legacy of his predecessor, and Taro Tanaka, a boy brought into the group by the volatile Serizawa Kamo. Together, these three form a younger generation within the Miburo, training alongside legendary historical figures including the gentle yet fierce warrior Isami Kondo, the passionate spearman Sanosuke Harada, and the serious narrator Shinpachi Nagakura. The series follows their struggles to earn respect, define their own sense of justice, and survive in an organization torn between its ideals and the harsh realities of violence and political maneuvering.

The story unfolds through several major narrative arcs. Nio's initial training and bonding with his fellow young members establishes the group dynamics before the series delves into conflicts with the Kyohachi dojo, a powerful swordsmanship school that becomes a recurring adversary. A significant arc focuses on protecting the young shogun Tokugawa Iemochi, called Kikuchiyo, a kind-hearted leader who challenges expectations of what a ruler should be. The first season concludes by setting up the "Serizawa Assassination Arc," a pivotal historical event that will reshape the Miburo into what would eventually become the legendary Shinsengumi. A second season covering this arc is scheduled for release in 2026. Throughout these events, the anime explores how a group of hated ronin gradually transforms into the shogunate's elite police force, with Nio as a fictional witness to this historical transition.