貴族の守護者ライジェル、彼の忠実な執事であるフランケンシュタイン、ユニオンの実験体だったM-21は、正体を隠したまま私立芸欄（イェラン）高校で日常を過ごしている。平穏な日常を送っていたが、ある日、高校に過激な集団が乗り込んできて…！生徒達を守るため、M-21は選択を迫られる。そして、その頃謎の戦闘部隊 DA-5 が、調査の任務を帯びて日本へ派遣され…。果たして彼らの平和な日常はどうなってしまうのか？

日本で起きた一連の事件を調査するため、貴族のレジスとセーラが芸欄（イェラン）高校にやってくる。ライジェルとフランケンシュタインは正体を隠しながら二人と接するが、レジスとセーラはM-21が改造人間であることに気づき、警戒する。一方、下校中に田代がまた不良とのケンカに巻き込まれ…。

ユニオンの特務部隊DA-5に捕まってしまったM-21。しかし、逆にこのチャンスを利用して昔の仲間たちに関する情報を探ろうと試みる。自分の思い通りにことが運ばないシャークは、M-21に替わる、他のターゲットを探し始めるが…。そんな中、田代とセーラは道端で困っていたタキオと偶然出くわし、加瀬はハッキング対決をしたタオと予想外にも意気投合する。

Seira realizes Regis is in danger and rushes to help him. Raizel and Frankenstein suspect that Tashiro and Kase might be in trouble as well, so they follow Seira. M-21 comes up with a plan to sacrifice himself to save all of them, and Regis confronts the danger by his side. The battle against DA-5 has begun! But they're up against the Union's state-of-the-art special forces team, an opponent that won't go down easily...

Frankenstein's battle with Takio and Seira's battle with Hammer grow more intense. Tao and Takio clash as Tao tries to keep Tashiro and Kase out of the conflict, but their leader, Crans, enacts an unbelievably brutal plan in order to win... Meanwhile, Raizel reaches M-21 and uses his overwhelming power to take on Crans.

Tashiro finds himself increasingly attracted to Seira, so he asks the other guys for advice. Unfortunately for him, the likes of M-21, Tao, and Takio are already a hit with the ladies, so their advice isn't very helpful, and Frankenstein only gives him boastful stories from his own history. Will Tashiro's plan to get his feelings across to Seira be successful?

Since contact with Regis and Seira has been lost, Regis's grandfather, Gejutel, heads to Japan on Raskreia's orders. Once he arrives there, he unexpectedly runs into Frankenstein and Raizel. Who were the Frankenstein and Raizel that Gejutel knew in the past? Are their true identities finally about to be revealed?

Raizel and Frankenstein first met in Lukedonia, the country of nobles. Raizel took Frankenstein, who was a noble hunter at the time, into his mansion to work as his butler. Frankenstein protected him for several years, but then some among the nobility who had unfavorable opinions of the duo began to revolt. What decision did Frankenstein and Raizel reach in response to this conflict?

Rael arrives at Ye Ran High School to collect Seira per the Lord's order, but he encounters M-12, Tao, and Takio there, and a fight breaks out. Who is this man suddenly confronting the three of them? Seira tries to persuade Rael to leave, but Rael continues to do as he pleases. And for the sake of protecting Raizel, Frankenstein can't just stand by and watch all this carry on...

Seira visits Lukedonia per the Lord's order. To protect Gejutel, she has no choice but to conceal the truth about Raizel. Raizel and Frankenstein finally decide to visit Lukedonia in person to settle everything, and M-21, Tao, and Takio follow them in secret. The welcoming of these unexpected visitors would be the start of chaos in Lukedonia...

Seira escapes the Room of Discipline to save Gejutel, but is forced to fight Rozaria, and Regis also heads for the castle to save Gejutel but is stopped by Karias. M-21, Tao, and Takio work together to hold off Rael so that Raizel and Franken can get to the Sanctuary. Fierce battles are breaking out everywhere in response to Raskreia's final decision to force Gejutel into eternal sleep...

Raizel finally faces Raskreia and the clan leaders in order to prevent Gejutel's punishment of eternal sleep and settle things down. When Raskreia faces Raizel, someone she has hated for most of her life, she decides to try to destroy him herself, but the clan leaders who serve her are unable to just stand by and watch. Only the Lord's soul weapon, Ragnarok, holds the truth about what happened in the past as the curtain rises on the battle between the Lord and the Noblesse.