In Prodigy, we see the specific actions that comprise a revolutionary effort to kick back against the tyranny of an overbearing construct of human invention. The novel is pointing to the problem with traditional power dynamics: they quickly insulate mischievous behavior, and in the case that an organization has supreme authority, the imbalance quickly turns to injustice and downright abuse of the citizenry, as in this book.
For June and Day, this divergence is clearly observable. June is a product of society, and Day is the victim of it. June has attained success in the tests elaborated by the government (basically a thinly veiled criticism of standardized testing), but since Day's life has been more disenfranchised, and since he is truly the victim of systemic injustice, belonging to a class of completely disenfranchised poverty. He doesn't have any of the advantages or privileges, but the novel shows that June is not evil for her privilege, because they agree that the community is in dire need of improvement, and they cooperate.
How far should one go for justice? That seems to be the question implied by the various characters who are martyred by their desire for justice. They rail against the empire-oriented Republic that insulates its own power and mistreats the poor and needy. So, their cause is true justice, it seems, because they want to preserve the rights of their communities against the pernicious overlords. For this effort, the novel seems to suggest the sacrifice for one's community is of ultimate value, because many characters die in exactly that fashion.
