Episode 1: Monsters in the Nightmare
The story begins in a ruined city after the catastrophe designed by god. After Dr. Sanders transplants Ayaka's “almighty cell” into her heart to cure her cardiac disease, Ayaka starts having a nightmare where she gets chased around by beasts. One day, she gets attacked by a beast in real life, and gets saved by a beast boy named Shinichi, also the savior in her dream. It turns out that Shinichi's father, Dr. Kuruma, used a secret DNA to turn Shinichi into a beast to create a New Human, and Dr. Sanders injected the same DNA into Ayaka's heart. So, whenever Ayaka is in danger, her heart calls for Shinichi's help.
Episode 2: Creatures in the Underground Complex
Tommy follows Ayaka to find out her identity and finds Dr. Kuruma, Shinichi's father and sworn enemy, is alive. Ayaka is attacked by Dinosaur Humans and kids try to help her. Shinichi believes that those kids have a pure, beautiful heart because they lost their parents in the catastrophe before they became their enemies as Shinichi's father did to him. However, when Shinichi gets there, the kids have been killed. Ayaka is now put up on a cross as a sacrifice to god.
Episode 3: Tower of Death
It turns out that Ayaka is being sacrificed to god because god needs Maria's blood for resurrection, but Maria is gone, and because Shinichi took in Maria's flesh and blood, Dr. Kuruma belives that Shinichi's DNA, incorporated into Ayaka's body, has the same effect. Shinichi fights a tough battle with the Dinosaur Humans, and Ayaka is taken into the Dinosaur Human's body. Although Shinichi is a beast, he has a human heart, so he cannot kill Ayaka. Then, Dr. Sanders shows up to show regret for what he did to Ayaka and uses a shot to release Ayaka from the Dinosaur Human. After the fight is over, Dr. Sanders asks Shinichi and Ayaka to run and hide until the “Awakening.”
Episode 4: New Beast
Tommy reveals his identity as the offspring of an ancient Hebrew tribe who left Jerusalem after being segregated as heretical by other god-believing tribes. Tommy and his 12 Generals are destined to protect god resurrected, and they show a statue which resembles Shinichi. However, Shinichi is not comfortable with the idea of god and Ayaka also believes that god is within all living creatures. Then, new monsters attack!
Episode 5: Prisoner
It turns out that Shinichi let his enemy take him to Rockwell's lab to find Dr. Kuruma. One of the enemy beasts, Swallow Tail, has a heart and is afraid of a heartless bug taking over her body, so she tries to escape with Shinichi. Swallow Tail takes Shinichi to a clone room where he finds many clones of Maria, which infuriates him. Shinichi fights a tough battle with enemy beasts, but Swallow Tail blows up herself to let him escape.
Episode 6: Revenge
Rockwell injects Shinichi's blood and god's cell to turn Defense Minister, Semi-Maru, into god. Semi-Maru betrays Rockwell, locks him up, and orders soldiers to find Shinichi and kill him. Semi-Maru's armored soldiers attack Tommy's house, a public train and even burn a whole town where Shinichi is at. In the meantime, Dr. Kuruma gets hold of Maria's blood, so now he can mix it with god's cell to form god, too.
Episode 7: A Person to Inherit
The military cannot read the isotope marker they planted in Shinichi to find him because Shinichi hides in a tank truck full of high density energy. However, by the time Shinichi reaches the military base to fight Semi-Maru, the Defense Minister with god's cell injected, Shinichi is weakened. Shinichi fights a losing battle against Semi-Maru, but then, Noa, a god boy sent by Dr. Kuruma, shows up to save Shinichi. Shinichi senses Noa's great power and Maria's light around him.
Episode 8: 4 th Interglacial Period
On a boat trip to southern islands, the image of Maria makes Shinichi realize that he did a right thing by taking in Maria, and that his new purpose in life after revenge on his father is Ayaka. However, Dr. Kuruma starts his Noa's Arc plan which causes tsunami in the ocean to wipe out human civilization on the ground, then to replace humans with god's clones, Noa. However, Noa turns out to be a failure, so Dr. Kuruma comes up with a new way to extract pure Maria's blood. Shinichi, Ayaka and Tommy survive the tsunami and start living on a deserted island, but then they get attacked by Leviathan. After Shinichi beats Leviathan, Kraken kidnaps Ayaka.
Episode 9: The Monster in the South Sea
Tommy notices that Shinichi looks alive when he's angry and remembers the legend of the statue that when god's power gets out of control, it becomes evil power to destroy humans. Noa is afraid of it, too, but Dr. Kuruma kidnaps and kills Ayaka to extract pure blood of Maria, which infuriates Shinichi. Shinichi fights a tough battle with a sea monster, Aspidkeron, but he combines with it and finally finds Dr. Kuruma in the underwater lab of Dr. Fisherman.
Episode 10: The Day of Deluge
Shinichi comes back to West Shinjyuku where kids defend themselves with weapons now. 2 powerful energy comes from the moon as in the time of the last great destruction. They are military gods, Adam and Eve, coming to the land of Armageddon on the Judgement Day to set up a stage for god's resurrection. But Shinichi is so powerful with rage that they beat the military gods easily. Now Neo-Noa, created by Dr. Kuruma, shows up and separates the wild beasts from Shinichi's body, and let them attack him.
Episode 11: Awakening of Son of God
Shinichi loses his beasts to Neo-Noa and fights a tough battle with him. Clone-Noa comes to help Shinichi because he was made by Shinichi's blood, but not well enough to beat Neo-Noa. Finally, spirits of Ayaka, Maria and Shinichi's mother come out of Shinichi and help him fight Neo-Noa.
Episode 12: Armageddon
Neo-Noa does not die and erases the spirit of Maria, Ayaka and Shinichi's mother. Shinichi loses the spiritual bond to them, and after winning the battle and absorbing Neo-Noa, he turns into the complete beast.
Episode 13: The Last Judgement
Shinichi turns into a beast, goes out of control and starts absorbing living creatures on the earth. However he sees light in the darkness when he reaches the kids he left behind in Shinjyuku. Tommy realizes his mission and shows Ayaka's pearl to Shinichi to tell him the fact that he can never bring back the dead but he must give the kids hope for the future. Shinichi seals himself with the evil black clouds to protect the kids. Tommy tells the kids that Shinichi will revive when god awakes in the near future.