"Samurai Harem" centers on Junichiro Tachibana, a young man who unexpectedly inherits the role of the "Last Samurai" after his grandfather's passing. This title comes with significant responsibilities, as Junichiro must protect the world from supernatural threats using his ancestral sword, the Muramasa. However, the sword's power is tied to a unique condition: Junichiro must form emotional bonds with several women to unlock its full potential. These women, known as the "Bride Candidates," each possess a fragment of the sword's power and are destined to assist Junichiro in his mission.

The narrative unfolds as Junichiro navigates his new role while balancing his relationships with the Bride Candidates. Among them are Ayame, a childhood friend and skilled martial artist; Rin, a mysterious and reserved girl with a tragic past; and Suzuka, a cheerful and energetic individual who brings levity to the group. Each character has a distinct personality and backstory, contributing to the dynamics of their interactions with Junichiro. As the story progresses, the group faces various supernatural adversaries, including demons and otherworldly entities, which test their resolve and teamwork.

The series explores themes of duty, camaraderie, and personal growth as Junichiro learns to embrace his responsibilities while fostering genuine connections with the Bride Candidates. The plot intertwines action, romance, and comedic elements, creating a balance between intense battles and lighthearted moments. The overarching goal is to restore the Muramasa's full power and prevent a looming catastrophe, but the journey is fraught with challenges that require both physical prowess and emotional resilience. Through their trials, the characters evolve, and their bonds deepen, shaping the outcome of their shared destiny.