Bird of Fire follows the story of the legendary immortal bird Phoenix as it witnesses and chronicles humanity's struggles for power, justice, and freedom throughout history. In ancient times, the cruel Queen Himiko of Yamatai sought the Phoenix's blood, which she believed granted eternal life, and her conquest of the Land of Fire left only Nagi, his sister Hinaku, and her foreign husband Guzuri alive. Nagi was taken prisoner, but Hinaku discovered a shocking revelation, while elsewhere in the future, humanity had colonized other planets due to an uninhabitable Earth.
In a distant future, Leona, a space station patient, received a cybernetic brain transplant after a fatal accident and began to see humans as faceless objects, while robots appeared to him as people. Leona fell in love with a discarded robot named Chihiro and escaped the space station with her to avoid destruction, but Leona's memories started to return, forcing him to confront a painful truth about his past. The Phoenix also appeared in other eras, influencing various individuals, including Sakon no Suke, a daughter of a tyrant ruler who killed a priestess to gain independence, and Prince Harima, a prince whose head was replaced with a wolf's after losing a war, who found refuge in a Wah village and eventually became a respected leader under the name Inugami no Sukune.