Hi no Tori follows the legendary Phoenix as it observes and documents humanity's never-ending pursuit of power, justice, and freedom, from the beginning of time to the distant future. Since time immemorial, people have sought the Phoenix's blood for the gift of immortality. When Queen Himiko of Yamatai hears rumors of its whereabouts, she launches an attack in search of the bird. Only Nagi, Hinaku, and her husband Guzuri survive the onslaught, but Hinaku uncovers a startling truth while they escape. In a bleak future, Leona becomes a cyborg, losing her memories and experiencing visual distortions. She falls in love with Chihiro, a discarded robot, and together they flee from the space station where they received their augmentations. However, Leona's recovered memories reveal a harsh reality. Sakon no Suke murders a healer to achieve independence for herself and her father. While seeking refuge in a priestess' sanctuary with her servant, she takes on the role of healer and wields a mystical feather. Persecuted by a monk, Prince Harima finds sanctuary in a Wah village with the help of a medicine woman and General Saruta. Under the guise of Inugami no Sukune, he thrives, but new threats arise. In a world decimated by disaster, Doctor Saruta and his companions learn that the automated system running the underground cities triggered a nuclear apocalypse.