The story centers on a newly appointed warden, Henry Brubaker, who goes undercover as an inmate to observe the corrupt conditions of a Southern prison farm. Upon entry, he witnesses rampant abuse, including physical violence, neglect, and a lack of basic human rights. Brubaker begins to understand the depth of the corruption as he experiences firsthand the brutality that the prisoners endure daily. As he reveals his true identity, he faces significant resistance from both the prison staff and the local community, who are heavily invested in maintaining the status quo for their benefit.

Once revealed as warden, Brubaker attempts to implement reformative measures to improve the inmates' living conditions and eradicate corruption within the prison system. His progressive ideas and unyielding determination put him at odds with influential figures in the community, making his mission increasingly difficult. Armed with a sense of justice and unwavering resolve, Brubaker challenges the deeply ingrained injustices, seeking to bring dignity and respect back to the prison. His journey is met with numerous obstacles, questioning whether one man's will can indeed make a difference in such a deeply flawed system.