Yakov starts the story with very limited freedom, and as the novel progresses, he faces even greater deprivations. At first, Yakov's options for where to live, work, and travel are restricted due to his Jewish identity. For a short time, by renouncing his Jewish roots, he gains some freedom to move beyond these limitations. However, this new freedom is fleeting, as he is soon falsely accused of murder. His imprisonment, which occupies most of the novel, deepens his confinement. He despises his initial cell because it leaves him vulnerable to the whims of other prisoners, but solitary confinement turns out to be even more brutal. Once he adapts to solitary confinement, his movement is further limited by being shackled to his bed. Throughout this ordeal, the cruel Deputy Warden subjects him to invasive body searches, inspecting Yakov's mouth and anus even though it's clear Yakov couldn't possibly have a weapon; even his body is not his own. As his time in jail nears its end, Yakov loses hope for freedom. However, on his way to the courthouse, he sees his fellow Jews defiantly lining the street against the Tsar's regime, which reignites his belief in freedom. "Where there's no fight in it there's no freedom," he reflects. "Death to the anti-Semites! Long live revolution! Long live liberty!"

The book explores a political conflict between Christians and Jews that is largely separated from the true beliefs of these groups. More importantly, it highlights Yakov's personal journey as he moves from feeling disillusioned to embracing his Jewish identity. At the beginning of the story, Yakov leaves the Pale of Jewish Settlement, feeling out of place. He tells his father-in-law, Schmuel, "Torah I had little of and Talmud less," though he learned Hebrew due to his talent for languages. With few job opportunities and after his wife of six years leaves him, Yakov is doubtful of the comfort his religious roots could offer. Instead, he chooses to rely entirely on himself, symbolized by keeping his tool kit while discarding his prayer items into the Dnieper River.

Ironically, it is the authorities who attempt to force a Jewish identity onto Yakov while he is in prison. They demand that he grows his hair long in the traditional Jewish style. They provide him with phylacteries, small leather boxes containing Hebrew scriptures, which Orthodox Jews customarily wear on their heads and arms. Yakov reads these eagerly to pass the time. They also give him a prayer shawl, which he uses for warmth. Their goal is to make him seem part of an Orthodox Jewish conspiracy, but during his imprisonment, Yakov starts to value his Jewish heritage. This change is clear at the end when he protests against having his Orthodox-style ringlets cut.

In this book, social classes often correspond to religious affiliations; Russian Christians hold the dominant societal position, while Jews are pushed into the lower class due to governmental restrictions. Yet, there are significant moments when religious differences are overlooked, allowing individuals to interact as equals. For instance, when Yakov first arrives in Kiev, Lebedev is struck by Yakov's character and diligence, offering him a job as an overseer in the brickyard based on his observations. Lebedev's own journey from poverty fosters a connection built on mutual understanding.

Later, while Yakov is imprisoned, he worries that his cellmates will hold him responsible for the child's murder he is accused of. However, the convict Fetyukov shows that, even though Yakov is from a lower social class, he does not subscribe to the superstitions about Jews. "When I was a boy, I was apprenticed to a Jewish blacksmith," he says. "He wouldn't have done what they say you did. If he drank blood, he would have vomited it up." A Russian Christian from a higher social class would probably not have had such interactions with Jews and might have believed the rumors. The most profound instance of class solidarity overcoming religious differences is Kogin's sacrifice at the book's end. With his own son imprisoned, Kogin feels more empathy for Yakov than for the Deputy Warden, despite technically being colleagues. Though Kogin had been indifferent to Yakov throughout most of his imprisonment, he ultimately sacrifices his life to save Yakov, recognizing that if the system can be unjust to one inmate, it could be equally unjust to his son.

Modern American readers are often taken aback by stories of individuals jailed for crimes they did not commit, with no external aid. The U.S. Constitution clearly guarantees the right to a swift trial, and organizations like the American Civil Liberties Union actively monitor any breaches of this right. Consequently, Americans usually assume that fundamental civil rights are assured, unlike in oppressive, totalitarian regimes where these rights are not acknowledged. In many countries, there is no guarantee of legal representation; in certain places, political prisoners suffer in cells while their families remain unaware of their status. Political prisoners are often executed under the weak justification of "attempting to escape," as Ostrovsky warns Yakov about in the book. Others endure torture and are then left with the means to take their own lives, as demonstrated with Bibikov. A sign of Tsarist society's recognition of prisoner rights is that in this novel, everyone believes Yakov will receive a trial once he is formally charged: a society without laws would not keep such a promise.