The irony of innocence
Justice is obviously not at the top of Tsar Nicholas II's agenda. Ironically, in an attempt to gain political power, Nicholas abandons the fundamental goal of government, to bring safety and justice to the citizens of the nation. Instead, Nicholas arrests random people just to pacify the victims of real crimes, without making an effort to actually solve the murder case. In Tsarist Russia, innocence and guilt are not what they seem.
The irony of the scapegoat
The idea of a scapegoat comes from pastoral cults like Judaism, where a literal goat or sheep is killed as a sacrifice to God for the atonement of the people. In the Jewish perspective, the "healing of the nations" is tied to this exchange of innocent blood for the guilt of many. At the end of the book, Yakov's ability to fairly scrutinize the government is his godlike gift for his service as a suffering servant. This complex religious concept is an attempt to make sense of another irony, the basic irony of suffering, that bad things happen to good people.
The irony of religion and "being religious"
Yakov's ironic plight is even more religious when his accusers try to make him admit that as a Jewish person, he might have hated Christians and murdered the boy for those religious reasons. But Yakov is only ethnically Jewish. He confesses that actually, he's not even religious at all. This is ironic, and so is the fact that the government naturally assumes that a peaceful religion might create a violent person.
The irony of authoritarian government
At the end of the novel, Yakov gets a chance to vent a little, and he accuses Nicholas II of being a poor leader. Ironically, the person with absolute power seems powerless to rule effectively or even to be successful.
The irony of the death of a Christian boy on Passover
Through their injustice, the Russian government in the novel actually defends a Christian family by scapegoating a Jewish carpenter during Passover and trying to kill him for a crime he didn't commit. These details make Yakov undeniably similar to Jesus Christ who was crucified during the same festival by a similar dictatorship. In other words, they accidentally create a Messiah character in an attempt to falsely accuse Yakov.
