"Rainbow Samurai" is set in a fictionalized version of Edo-period Japan, blending historical elements with supernatural themes. The narrative centers on a group of seven ronin, each wielding a unique sword imbued with mystical powers tied to the colors of the rainbow. These warriors, bound by a shared tragedy, unite to combat a shadowy organization seeking to exploit ancient artifacts for malevolent purposes. The story unfolds as they navigate a world rife with political intrigue, betrayal, and supernatural threats.

The protagonist, Akio, is a stoic and skilled swordsman wielding the Red Blade, a weapon said to embody the essence of fire. His tragic past, marked by the loss of his family, drives his quest for justice. Alongside him is Haruto, the wielder of the Indigo Blade, a former nobleman turned rogue, whose cunning and strategic mind often guide the group. Kaida, the bearer of the Violet Blade, is a mysterious and enigmatic figure with ties to the supernatural, her motives often shrouded in ambiguity. The group is rounded out by four other ronin: Renji, the brash and impulsive wielder of the Orange Blade; Sora, the calm and composed master of the Blue Blade; Yumi, the compassionate and healing-focused wielder of the Green Blade; and Tetsuo, the elder statesman of the group, who wields the Yellow Blade and serves as a mentor figure.

The plot is driven by their pursuit of the "Rainbow Shards," fragments of a legendary artifact that, when combined, grant immense power. The antagonist, Lord Kurogami, a corrupt daimyo with ambitions of domination, seeks these shards to unleash chaos. The ronin must confront not only Kurogami's forces but also their own inner demons and conflicting loyalties. Each character's backstory is gradually revealed through flashbacks, adding depth to their motivations and relationships.

The series balances episodic adventures with an overarching narrative, as the ronin travel across Japan, encountering allies and enemies alike. Themes of honor, sacrifice, and redemption are explored as the characters grapple with the moral complexities of their mission. The climax sees the group facing Kurogami in a final, decisive battle, with the fate of the nation hanging in the balance. The resolution ties together the personal arcs of the ronin, offering closure while leaving room for potential future developments.