The guards are corrupt, beating prisoners to death, officially listing their cause of death as "illness", and often receive bribes from inmates. The prison is seen as a way to make yakuza and other dangerous criminals "disappear" with no questions asked.
After 25 years on death row, Taiga Saejima is transferred to the penitentiary, run by Saito, a brutal and vindictive guard. He and Goh Hamazaki, who also resides in the prison, make their escape with the help of Renta Kamiyama's grappling hook.
When Hamazaki finally washes ashore and tracks down Kazuma Kiryu, he reveals that the documents stolen from the prison (intended to use as leverage to negotiate his freedom) detail a money laundering scheme; the ten billion yen, which Kyohei Jingu had taken from Toto Bank (and Shun Akiyama had taken the fall for), was part of a police scandal intended to create a "utopia" where they could send yakuza to have control over crime. The Snake Flower Triad had been involved in the laundering of money for the police higher-ups, something that Hamazaki had known about due to his partnership with the Chinese mafia.