"Hyakka Ryōran Samurai After" is a sequel to the original "Hyakka Ryōran: Samurai Girls" series, continuing the story in an alternate historical setting where Japan is divided into feudal territories ruled by powerful warrior clans. The narrative centers around Muneakira Yagyu, a skilled swordsman and the last master of the Yagyu Shinkage-ryu school of swordsmanship. Muneakira becomes entangled in a conflict involving the Tokugawa shogunate and a group of female warriors known as the "Master Samurai," who possess unique abilities tied to their spiritual connections.

The story begins with Muneakira encountering Jubei Yagyu, a mysterious girl who awakens as a Master Samurai after a kiss from Muneakira. This event triggers a series of battles and alliances as various factions vie for control over Japan. The Master Samurai, including characters like Sen Tokugawa, Gisen Yagyu, and Yukimura Sanada, each have their own motivations and loyalties, adding complexity to the political and martial struggles. The series explores themes of loyalty, honor, and the clash between tradition and progress, as the characters navigate their roles in a rapidly changing world.

The plot intensifies as Muneakira and his allies face off against the Tokugawa shogunate, led by the ambitious and cunning Yoshihiko Tokugawa, who seeks to consolidate power and eliminate threats to his rule. The Master Samurai must confront their own pasts and the consequences of their actions, while Muneakira strives to protect those he cares about and uphold his ideals as a swordsman. The series blends action, drama, and elements of historical fantasy, creating a dynamic and engaging narrative that builds on the foundation of its predecessor while introducing new challenges and character developments.