This game is not so much about justice (though it deals with characters that have lost hope in justice). I see in it several themes that seem more important:
- What makes us human? MB compares 'decency, honesty, love' to limbs: appendages that are not necessary to define a human being (you're a human being even if you lose them), but that are 'appropriate' to human beings. They are, as MB says in one of its most memorable quotes, 'for those who have the richness of heart to believe in them'. They are an outgrowth of our humanity that shows how far we can go -- even though we're still human without them.
- What is love? Several characters claim to act for 'love'. Valentinos is the 'hammer of the church,' who exterminates 'threats to God' and punishes 'sinners' so that (God's) love can survive and thrive. He loses; and I think the game makes it clear that his viewpoint is wrong. The main antagonist, 'Jane Doe' (the girl with different-color eyes), wants love to be "agape", i.e., love of a superior Being for all of creation; she wants to create perfection and a world without pain, a paradise on earth, and it is to this goal that she sacrifices the Disaster Witches in such horrible ways (she clearly thinks that the ends justify the means), but she is also incapable of accepting individual love, so she despises Shimon for loving her. Carol, on the other hand, loves Shōgo and believes in the mutual salvation implicit in that love -- and Shōgo, even if he won't admit it, also loves her, enough that, in the Ashes and Diamonds ending, she is saved, pregnant with his son. This is eros, or individual love. Are these things worthy of the same name -- Valentinos' "instrumental" love ('do God's wil, be His weapon,l and smite His enemies!'), Jane Doe's agape ('save the world!'), or Carol's eros ('save Shōgo')?