To be nice, I will admit that your writing has improved from your first stories.
However, that is a pretty low bar to clear.
Story Telling:
Your storytelling abilities are profoundly lacking. You seem to have no grasp on tension or narrative flow - it is nothing but a lifeless series of events without depth. World-changing events, such as two World Wars and the events of the End Time are rushed over in one threadbare paragraph or two. The exposition is hamfistedly shoehorned into the dialogue.
Characterisation:
Characterisation is extremely weak, especially in the human characters. Any form of character "development" takes the form of a sudden and radical change, at times due to stimuli that seem altogether insufficient for such a response. Furthermore, the characters are very lacking in depth, and indeed do not seem to have barely any personality or motivation of their own, being exchangeable and obviously just doing what the plot demands. Even the motive rants of Hercules and Lillith feel tacked-on to serve as strawmen, whereas their actual motivation seems to be "being Evil". There is very little nuance, and what little nuance there is appears to be entirely unintentional, caused by your own rather skewed perception of right and wrong.
I also note that there are... issues in your treatment of women in your story.
Pomme neither says nor does anything outside of her function as your wife or Jacob Jr's mother. Indeed, the only thing of any significance she does is giving birth to Jacob Harrison Jr., who is in himself a fairly minor and indirectly significant character, although even he still manages to have more impact despite less screen time. In the last few mentions, she does not even appear to be an individual anymore, but a dual entity consisting of her and her husband.
Anne is an even more superfluous character. She takes no action of her own, and her very few lines could just as well be given to Jacob. She is presented as a nun and faith healer, but these are informed attributes - at no point does she demonstrate any special connection to God or heal anyone.
Worst of all is Jacob Jr.'s wife/Anne and Jacob III's mother, who does not even get a name, let alone an actual appearence.
Your author avatar is a blatant Mary Sue. If your intention with killing yourself off early was an attempt to hide this self-aggrandisement, it backfired, as you had yourself declared a Saint and greatly influenced event even in and indeed beyond dead. The fact that both the heir to the throne and the protagonist are your off-spring bearing your name does not help against this perception, either.
Style:
Your style is extremely bland and boring. Beige prose is rampant, and everyone speaks in the same unrealistic voice.
Plagiarism:
Every good thing that could be considered positive is not your own, but the chapters you have copied nearly in their entirity with nary a change safe for replacing the protagonist's name and decapitalising "Old Gods" (on that, see my commentary in chapter 5) from Niam. And the few times you actually changed a few things, your beige prose and corny dialogue becomes all the more apparent in contrast to Niam's writing.
Conclusion:
I think the revelation that the Pope was Jacob's executioner could be interesting if handled by a more capable writer. In particular, this could be a good opportunity to flesh out Anne. Maybe, have her, as a nun, stay more loyal and defensive, if not necessarily towards Aksakallı - although she might argue that he is a changed man now -, then towards God and the Church, in conflict to a Jacob III instantly consumed with rage and desire for vengeance. But by all means, this does not mean she could not ultimately be turned around as well; indeed, for her who had sworn her life to the Church, this crisis of faith would be even more profound than for Jacob.
But, to be brutally honest: You are entirely untalented in every aspect of writing and probably should just give up for good.
