As the story begins, the three riders transform to fight Orphenochs. Mari catches up to them as the fight concludes and begs Takumi to return home with them. He returns home with her. Lucky Clover wants to recruit Yuka as a member. She is strong and has the potential to become stronger. Yuka, Naoya, and Keitaro volunteer with the kids at an orphanage where Teruo, the boy Naoya saved, lives. Strangers warn the police to quit investigating the “incidents” because they are accidents. Meanwhile, those same strangers continue to follow Yuka and her friends as they head to an amusement park. The strangers seem to be conducting experiments of some sort. Keitaro tries to make a move on Yuka and gets rebuffed. She runs off and is followed by one of the strangers. She is approached by Lucky Clover and is forced to fight to show her strength. Masato and Takumi come to her aid.

The strangers are a part of the police department. They are conducting experiments with the idea that the human component can be extracted from the Orphenochs allowing them to kill the monsters. Yuji and Takumi decide to talk to the police. They believe they can convince them that not all Orphenochs are bad. Mari is afraid that she will eventually become an Orphenoch because of the Smart Brain experiments. Masato assures her that the experiment was a failure. Yuka turns herself into the police in hopes of keeping her friends safe. She is brought to the secret research facility. Takumi and Yuji meet with the police and offer to trade themselves for Yuka. An Orphenoch already at the center rescues Yuka. Takumi and Yuji come upon them and allow the Orphenoch who helped to escape. After Takumi answers Keitaro's call, Yuji and Yuka are surprised by the police. The show concludes with Takumi defending the Orphenoch who saved Yuka.

Yuji begins to wonder if humans and Orphenochs can live together. Osada goes to live with Mari and Keitaro. She realizes that Keitaro is her pen pal. She runs away and the others search for her. The police search for her and Yuji. One of the Lucky Clover approaches her after Keitaro finds her. Yuka transforms and defends Keitaro. He sees her true form. Meanwhile, Yuji and Takumi are fighting off Orphenochs and police that are trying to capture them.

Yuji and Takumi manage to escape. Yuka tells Keitaro she left because she didn't want to be a burden to him and the others. He hugs her and tells her he thinks that humans and Orphenochs should live together and be happy. Takumi and Yuji continue to disagree about humans and Orphenochs being able to live together. During the fight with Bat Orphnoch, Yuka is ultimately wounded by humans and killed by at arms at Saeko.

After Yuka's death, a devastated Keitaro cries and mourns over Yuka. Kiba sees Yuka's dead body and thinks the humuns killed her. Takumi talks with Keitaro and Mari about Yuka. Then the King shows up and kill the man in rage. During a fight with the Bat Orphnoch, Faiz assumes his Axel Form and defeats the Bat Orphnoch, then Kiba changes into Horse Orphnoch and kills the police in a berserk rage and takes the throne of the President.