Sengoku Youko: Yonaoshi Kyoudai-hen follows Shinsuke, a samurai who stumbles upon the world of katawara, magical beings, and their interactions with humans. He witnesses Jinka and Tama, a powerful duo, battling evil and is drawn into their fight for justice.
Tama, a fox girl, can share her powers with Jinka, and together they right wrongs committed by both humans and katawara. Shinsuke joins them on their journey, learning about a darker side of humanity involving unethical experiments performed by monks.
The group, which grows to include Shakuyaku, a victim of these experiments, and other allies, sets out to make the world a better place, each driven by their own personal goals. Their journey involves confronting corrupt individuals and uncovering secrets about the relationship between humans and katawara.