There is an obvious comparison to be made between Yakov Bok and the historical person of Jesus Christ. For instance, both are Jewish, living under political oppression. Both are carpenters. Both are scapegoats for the injustice of an authoritarian regime. Both are on trial, although they are innocent. In both accounts, they are seen as despised and forsake. Their only loved ones mistreat them, but ultimately, they resist their oppressors and succeed in enduring their unfair mistreatment.
This messianic idea seems to be the central theme of the narrative, leading to the climactic moment when the scapegoat unleashes his anger against the leader. For Yakov, this means an imaginary conversation with Nicholas II, but just because the conversation is imaginary, that doesn't make it meaningless. By associating Yakov with messianic character traits, the author elevates that final rebuke to a position of religious authority.
At its core, the function of the narrative is to demonstrate the corruption and failure of Tsarist Russia in the early 20th century, by exposing its heinous practices and by openly criticizing Nicholas II openly. Even though the book wasn't written until 1966, The Fixer can be seen as a political commentary against certain similar elements of Russian politics during the Cold War, or perhaps just against Russian authoritarianism in general.