In the glimpse of the events that led to a myriad of horrors, John is at his happiest when "playing Jesus". Then the nun turns up, and he worries he was "going to get the Antichrist bit from her too". She doesn't accuse him of being the Antichrist, but somewhat perplexingly she then immediately tells him to stop doing what Jesus did.
It's worth noting that Jesus is pretty keen on the whole not keeping office hours and bringing the heat down on everybody thing. (So I do have some questions about the nun's hermeneutics.) Like, He says this, multiple times. Jesus is very, very clear that he's here to do miracles outside of office hours and that everyone who follows him is going to die badly. In Matthew 16, immediately after that explanation, comes one rather famous verse:
For what doth it profit a man, if he gain the whole world, and suffer the loss of his own soul? Or what exchange shall a man give for his soul?
Just as well no one significant in this story literally maims his own soul to gain the earth, eh?
So the nun helps (!) John find the soul, and just before tells him "Fear doesn't help us achieve a state of grace." Grace is basically being on a wavelength with God - in Christianity, grace is understood as something like God's love reaching out, and the human response to grace is central to various Christian understandings of salvation. So in Catholicism, a "state of grace" is where you're at when your soul isn't burdened by sins that prevent you being on that wavelength with God (e.g. after baptism or confession), it's the state of the souls that enter heaven. (It's also, per Tamsyn Muir, the state Gideon is in when she "shed eighteen years of living in the dark with a bunch of bad nuns", forgave Harrow, and Stanley Yelnats'd her father's rather catastrophic failure to respond to grace 10k years previously...). Grace, in the Christian understanding, is foundational to the possibility of forgiveness.
Shortly before Harrow turns to face John and walk backward into the River, he tells her "There can be no forgiveness for those who walked away...just as there can be no forgiveness for me." And then, speaking of the RBs, he says "Something will satisfy them eventually, but nothing satisfies me. Nothing." (Something, something, Romans 6:21...). And then he pivots, and says "that's the grace of it, Harrow. If I'm God, I can start over." For John, grace isn't about responding to something greater than himself, it's "A child's plea. Nobody has to know." It's an unwillingness or inability to face his own limitations and mistakes. It's a terrible fear that your sins will find you out. He gained the world and despite becoming god-emperor of space, it hath not profited him much.
So a huge part of the genesis of the entity that is John and the world he has created is conceptually predicated on a failure to respond to grace; the rejection of the possibility of a love that reaches out beyond all actions and boundaries to allow the possibility of forgiveness. In Catholicism, the only sin that can't be forgiven is the utter rejection of the possibility of forgiveness. And it's not incidental that John refers to Lyctorhood - his Lyctorhood, and the Lyctorhood he deceives others into - as an "indelible sin".
I've said before that John isn't The Antichrist, but he is an anti-Christ figure. So much of the world he presides over - metaphysically, structurally - depends on reversals of concepts in Christianity: a Lyctor consumes the body, blood, and soul of another mortal for a cursed eternal life; nuns pray the tomb is shut forever and the rock is never rolled away; people keep saying "it is finished", and it isn't.
Which brings us back to the Eighth... To Mercymorn, who unstitches the man who became god on an atomic level and quotes the last words of Jesus on the cross, perhaps drawing on some ancient memory from the woman whose soul she consumed. The Reactor article on the Houses says of the Eighth: "As the font of mortal forgiveness for sin, they take great pleasure in withholding mercy and pronouncing judgment." This is no doubt in part a commentary on institutional churches as a whole, and the murky business of fallible human beings attempting to mediate something transcendent. But there's something terrible and sad in the echos of Catholicism in the lives of both Cristabel and Mercymorn. The nun who urged John to allow grace to act in him became the founder of a House that grasps after some memory of the concept of absolution, under the gaze of a god who believes "once people see you do something and come to an opinion about it, there's nothing you can do. People don't forgive, not really". Mercy kills John and says "He was right. There can be no forgiveness." John dies (however temporarily) because he could not imagine a world in which forgiveness was possible, at the hands of the woman who once sacrificed herself for him.
If grace is the love of God, and perfect love casts out fear, as another guy called John once said, one man's fear has cast out love from the entire edifice of the religion built around him. What does it mean that forgiveness is so central to Gideon's story? Just what is Silas Octakiseron, Master Templar of the Forgiving House, going to do in ATN, having yeeted himself out of purgatory to go find his cavalier in hell? The place Harrow may be...well...harrowing? If grace is the love of God, and we have not yet begun to see the horrors of love, just how scared should we be for ATN? Especially when Harrow ended NTN with the words "O corse of the Locked Tomb, I have loved thee all my life, with mine whole soul, and with mine whole strength. I would to God that I find grace in thy eyes. Destroy me according to thy word, for I love thee."?
(And does this have anything to do with Muir's fears of excommunication?)