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.

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 .

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.

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 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.

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.

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.

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.

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 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 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.

After rescuing Jeanne, Shinobu acknowledges her ideals and invites her to join the Seven Light Faith. Meanwhile, Tanganika, the precious mage of Imperial General Neuro, unveils his hidden power, laying death and destruction to his surroundings in an ample display of the empire's might. To counter him, the world's greatest politician, Mikogami Tsukasa, executes his prearranged plan lighting the beacon of revolution in this other world. "We will defeat the empire and carry out our revolution." Tsukasa then speaks on the new world, the new nation they'll create before the crowd gathered around him.

A small customer arrives at Etranger: second-year grade school student Kasaka Hajime. Hajime asks for a gemstone like the one he has and pulls an unset Cat's Eye out of his bag. Seigi is surprised and attempts to question Hajime about his situation, but Hajime obstinately refuses to speak to Seigi, who treats him like a child. Meanwhile, Hajime slowly begins to open his heart to Richard, who treats him like a customer...

As Main and Lutz begin making their paper for real, Main's excitement gets the better of her, and Lutz's suspicions come to a head. He resolves to talk about it after the paper is finished.