Newly appointed Arkansas State Wakefield Prison warden Henry Brubaker arrives at the penitentiary disguised as a prisoner, joining a bus full of new inmates. He quickly finds himself navigating the grim realities of prison life: insufficient beds, appalling food quality, malfunctioning showers, rampant sexual violence in the barracks, and cruel punishment methods. The scene becomes particularly riveting when Brubaker discovers a maggot in his meal. Later, he learns of inmate Larry Lee Bullen being taken away under the guise of a phone call only to be brutally beaten.
On sanitation detail, Brubaker and the injured Bullen wrestle with the putrid conditions outside Death Row, where things escalate when inmate Walter takes Bullen hostage, demanding to speak to the warden. After calming Walter down, Brubaker reveals his true identity, surprising Walter, who reluctantly lists his demands for better living conditions, including yellow-painted walls and a television like those reserved for the corrupt convict guards. Once their meeting ends, Brubaker ensures Walter is locked back in his cell, setting the tone for his leadership.
Trusty Dickie Coombes later guides Brubaker to the office of Warden Renfro, played by Lee Richardson, where Brubaker announces Renfro's termination from his position. Following this, he faces the prison crowd, introducing his new rules amid the scrutinizing gaze of governors' assistant Lillian Gray and Prison Board Chairman John Deach. While Deach insists on staying informed, Lillian cautions Brubaker to tread carefully.
As Brubaker transforms the prison's environment, he compels Death Row prisoners to enjoy sunlight for brief moments, yet soon learns about unfortunate events, such as the roof collapse in the barracks during a rainstorm. His determination leads him to save injured inmates despite facing challenges in getting ambulances to respond. In the infirmary, he discovers that the medical staff exploits inmates by charging for services. Taking swift action, he replaces the doctor who had long taken advantage of the system.
Brubaker investigates the kitchens, realizing there's blatant mismanagement as food meant for inmates is being misappropriated. When C. P. 'Woody' Woodward visits, he requests the rebuilding of the barracks’s roof for free, but Brubaker stands firm, stopping the practice of free labor that benefits the local contractors. Woody's warning that there will be consequences for Brubaker's resistance becomes apparent as he struggles with deeper issues involving corrupt prison labor and stolen food supplies.
When Brubaker uncovers a hidden cabin occupied by trusty Huey Rauch and his girlfriend, who were hoarding stolen supplies, he takes decisive actions against the bureaucratic negligence surrounding such theft. Building an inmate council comprising trusted inmates, Brubaker aims to regain order and transparency. However, his reforms fizzle as trouble brews among the trusties, leading to violence against inmates like Abraham who dares to speak up about the buried secrets of the past.
His quest for justice pushes against the system, which comes to a head during a Prison Board meeting where it's evident that profit and corruption are prioritized over inmates' well-being. Brubaker becomes increasingly frustrated with Lillian and the board's reluctance to confront the ugly truths of the prison system, and the situation escalates further when he discovers Abraham's lifeless body. In a desperate move to uncover hidden truths, he orders the innocent inmates to search for buried bodies, risking their safety in the process.
Brubaker's resolve intensifies when he realizes the deep-rooted corruption reaches into the highest levels of authority. Every attempt to reform the prison leads him into conflict not just with inmates, but with the very structures meant to uphold justice. As he faces off against powerful figures like Senator Hite, Brubaker insists that accountability must come first.
Confronted with the fallout of his decisions, Brubaker learns a startling truth about current inmates and their connections to the past. The violence peaks when Rauch murders Bullen, leading to a tense showdown. By the end, as Brubaker faces repercussions for his brave stance against the system, the respect he garners from the inmates shines through; their applause marks a poignant farewell to a warden who dared to challenge the status quo, as Dickie leads the charge in honoring Brubaker's efforts.
