>>280458265
Nagi's plotline is just a carryover from Kichikuoh, but they want to work in a happy ending for both Nagi and Shizuka somehow. Plus Nagi getting raped by her biological father is part of her character.
Although X Part 2 is literally a generic self-insert incarnation fantasy adventureslop with an *extremely heavy* emphasis on incest, so maybe it's part of the grand design. The twist is God is the one who self-inserted and the whole thing is a ploy to make it take a liking with generic fantasy adventure (and incest) instead of watching a misery simulator from the sidelines.