Sacred stones are implanted in the bodies of two boys. Decades later, the world is divided. There are those who want to eliminate the "kaijin" and those who want to coexist with them. In the midst of this, there is a man, Kotaro Minami who’s somewhat a recluse. A young activist, Aoi Izumi wants to change the divided world. When Aoi and Kotaro meet, the time which had stopped begins to move again…

Prime minister Shinichi Dounami wields his power, as he lines his pockets through the kaijin business, taking advantage of the needy and minorities. The Gorgom Party, a political party linked to Dounami, sends an assassin to Kotaro with an order to recover the Kingstone. Nobuhiko takes action, but what is his true purpose?

After the attack, Aoi and Kotaro find themselves in a strange relationship. Meanwhile, Bilgenia, who had obtained video evidence from Kawamoto, the wanted man doesn’t tell Dounami about it. In the midst of all this, the protest that Aoi participates in develops into violent clashes and chaos. Then suddenly Nobuhiko Akizuki appears, insisting on the rights of the kaijins and rousing them to action.

Nobuhiko, together with the kaijins he gathered, tries to recover the former Gorgom. An old friend visits him and informs him that the Kingstone is under Aoi's care, so he goes to Kotaro... Meanwhile, Aoi is happy to see her father, Hideo Kawamoto again. However, Aoi is suddenly pursued relentlessly by her father who has turned into a kaijin. But she is saved by an unexpected person.

Kotaro remembers Yukari's words about defeating the "Creation King". In his hometown, a facility for experimenting on kaijins remains, and Bilgenia awaits them. Aoi and her mother are taken captive. Kotaro tries to rescue them, but a "Mantis"stands in his way. In the battle, he learns the truth and his hatred for Bilgenia grows, causing the Black Sun to manifest new powers.

Kotaro confronts the "Creation King" once again. That meant facing the abominable past and everything was supposed to be settled. In front of the king's corpse, Nobuhiko is informed of the truth about Yukari. Meanwhile, Aoi and Shunsuke succeed in escaping despite losing various things. But on their way home, after parting ways with Aoi, Shunsuke is surrounded by an anti-kaijin group...

Rino, who has prepared for her own demise, entrusts "Nomi" with a "key", and he hands it to her daughter Aoi. Aoi is reunited with Kotaro after he regains consciousness, and she tells him with a smile that she has protected the Kingstone. Nobuhiko, who has risen to a new pinnacle by denying Darom's methods and crying out for change in Gorgom, points his beloved road sector back to his hometown.

Nobuhiko, who has attained power over the kaijins, notifies Prime Minister Dounami that humans should take their place under their command. Meanwhile, in the sea cave where "kujira" is still providing treatment, a miracle occurs thanks to the power of Aoi, who has joined them. Kotaro, who is regenerated by the miracle, utters the words "heat heaven" with a strong will.

Black Sun transcends time and soars in the sky. Believing in his own justice, he heads to overthrow Shadow Moon for the sake of the planet. The two throw themselves into the final battle for their destiny. After a fierce battle, Nobuhiko entrusts the Kingstone to Kotaro and returns to Yukari. But behind the scenes, a shadow that had been watching the whole thing is lurking suspiciously...