A boy named Nagi lives in at the foot of the mountain where the Phoenix resides. His sister, Hinaku, is saved by Guzuri, a medicine man, falls in love with him. At the night on their wedding, the village is suddenly attacked by troops of Yamatai led by Sarutahiko. The truth is then discovered: Guzuri has double-crossed them.

Frightened by coming of old age, Himiko, the Queen of Yamatai, desperately wants the life-blood of the Phoenix. Sarutahiko who won the war brings Nagi with him. He trains Nagi as a hunter for the Phoenix. Nagi, however, is planing to attack Himiko instead, while Sarutahiko is accused of such Nagi's act. Nagi rescues Sarutahiko from the Hornet's Cave and heads for his homeland.

In search of the Phoenix, Yamatai troops surge into the volcano. Among them is a master of archery who confronts Sarutahiko, but their fight ends in a draw. Sarutahiko asks Yumihiko to give up the Phoenix to Nagi if he succeeds to capture it. Yumihiko finally shoots down the Phoenix while the volcano is shooting out the fire. But Himiko dies before she can sip the life-blood of the Phoenix.

With the help of a woman named Uzume, Nagi and Sarutahiko escape from the horse-riding tribe which aims to destroy Yamatai. Back in the Yamatai Kingdom, they battle against the horse-riding tribe together with Yumihiko but they are outnumbered.

In the 25th century, Leona involved in explosion at the laboratory on the moon, is restored to life with artificial brain planted in. He, however, has lost his memory due to the effect of the operation. Furthermore, people become to be reflected as debris on his eyes.

While Lamp doggedly follow Leona, Leona and Chihiro subconsciously reach the explosion site in the research facility where Leona gradually retrieves his memory in the past. He recalls his father who died in hopelessness, his revolts against such his father and a research on the vital energy in the Phoenix's feather conducted by Dr. Saruta .

Sakon-no-suke, a woman who has been brought up as a male, sets off to kill Yaobikuni who tries to save her diabolic father. After killing Yaobikuni at a temple, Sakon-no-suke cannot return home, and finds out Yaobikuni is herself in the future - trapped in the circle of time.

Defeated General Harima is forced to wear a wolf skin over his head which cannot be taken off. He heads to a country called Wah together with Obaba who has helped him and an injured General Saruta, where they save a girl named Marimo, a daughter of a canine tribe worshiped as a native god. While resting in a village that Saruta has known, they are assaulted by attackers.

Harima who has changed his name to Inugami-no-Sukune, becomes the leader of Inugami village where village folks enjoy prosperity. It seems like the peaceful life in the village lasts forever. However, pressures from the Imperial Court to exclude native gods to extend Buddhism rapidly increases. Just then a holy seat enshrining a native god is hardly destroyed by a minister's followers.

After the death of Emperor Tenchi, the political situation starts to change significantly. Inugami, who was saved by Marimo, has recovered from his wounds. With resentment against repeated orders for labor and contributions imposed on the villagers, Inugami again heads to Otsu, but is arrested for violent behavior towards a minister.

A battle between the army of Prince Otomo and that of Prince Oama, Hirafu, and Inugami breaks out. Prince Otomo attacks Inugami with paranormal powers utilizing Buddhism while Marimo and her canine tribe members, together with other native gods, support Inugami. The Phoenix, however, refuses to stand by Inugami.

After escaping from an underground city called Yamato, Masato and Tamami make it to Dr. Saruta, an authority on artificial beings. A full-scale war between underground cities breaks out, resulting in the extermination of the human race.

Masato is all alone left in the world and is tormented by overwhelming loneliness. A long, long time passes, and a new life is born from Masato himself. At last, he reunites with Tamami.