In the port town of Shoubara, the legacy of legendary yakuza boss Murata Kyousuke looms large, but it is his only son, Kyoutarou, who takes center stage in this story. A high school student by day and a ruthless gang leader by nature, Kyoutarou runs a criminal enterprise that includes poaching, running hostess clubs, and forcing prostitution on female students, all while carrying a handgun with impunity. Despite his fierce reputation and the fear he instills in the local underworld, he maintains a facade of a good son in front of his mother, Kumiko.

The central conflict ignites when Kyoutarou attacks a local yakuza office, an act that lands him in the news and before a judge. His father, Kyousuke, now the powerful don of the Souwa Alliance, makes a solemn vow to prevent his son from inheriting the bloody destiny of a yakuza. To break Kyoutarou's unyielding spirit, Kyousuke arranges for his son to be sent to a notoriously corrupt prison. He hires a rogue operative named Ootomo Ryuuji to get himself arrested and placed in the same facility, where he is tasked with beating Kyoutarou into submission.

The prison arc becomes a grueling test of wills. Ootomo and his men torment Kyoutarou relentlessly, even framing him for assaulting a guard to isolate him from his visiting mother. Confined to a straitjacket and thrown into solitary confinement, Kyoutarou refuses to be broken. In a moment of vengeful fury, he pours boiling tea over Ootomo’s head. The dynamic shifts when a massive earthquake strikes the prison. Amidst the chaos, Kyoutarou takes command, ordering guards and inmates alike to rescue the injured and prevent a mass escape, even as a tsunami follows. Using blackmail evidence of the guards' abuses, he secures parole for everyone involved in the rescue.

Throughout this saga, Kyoutarou clashes with his uncle, Kentarou, a straight-laced police officer, and terrorizes a sadistic student teacher named Yagisawa Yuichi. He also shows a protective instinct, avenging a girl named Hidemi who has feelings for him. Ultimately, Shin Otokogi is a hardboiled tale of a delinquent son and his yakuza father locked in a violent struggle, with the father trying to save his child from a life of crime by any means necessary, only to find that the son’s wild nature may be impossible to tame.