Children of an Elder God by John Biles and Rod M.

2026 Update: I have an apology to make. I shouldn't have recommended this, because I wasn't actually comfortable with the content. I also really shouldn't have been so oblique about the sexual content warnings, even if I didn't know how to phrase that section without making it seem more intense than it seemed to me at the time. I did like some parts of it quite a bit (the first chapter with the light-versus-darkness energy fields followed by the giant robots mutating to take aspects of their destroyed foe, and also the reinterpretation of LCL as black foul-smelling sludge, plus one scene near the end where Fishwoman Ritsuko Akagi is obliged to kill her mother right after the first nice thing her mother had done for her, which was offer to shelter her and Maya Ibuki during the apocalypse - and curses her for that kindness in such a melancholy way -) but other scenes have stuck with me which I wish had not. It may also be lost media, given the broken image link. Aside from the Sexual Content section, this review is unedited; you get to read a much younger me's phrasing choices.

Another review!

I liked Children of an Elder God quite a lot, but I do need to warn you about some of the content.

• Setup: Neon Genesis Evangelion with the Pseudo-Christian parts replaced with the works of  Howard Phillips Lovecraft (and successors).
• Execution: Like I said, I liked it, but it is fairly faithful to both universes, so not exactly kid friendly all the time.
• Swearing: Bad, the main characters are both teenagers and soldiers, and it is handled mostly realistically, F-Bombs are dropped infrequently, as well as D-words and S-words, both English and German.
• Violence: Again, the Cthulhu Mythos and Neon Genesis Evangelion, together, portrayed fairly faithfully, so you should not be surprised that body horror, blood, and eldritch abominations being eaten by humungous mecha abound.
• Sexual content: More than I was comfortable with, and on reflection, more than I'm comfortable with in a story I recommend (hence the uncertain tone of this post for the last 14 years). Though kept mostly offscreen, there are a couple scenes I've had cause to regret having read. Rape is a recurring theme, as is sexual degeneracy as synonym for the influence of evil powers; either one able (somehow) to transmit the other.
• Religious/Others: Talk of eating souls, "beings" called Outer Gods, talk of cults worshiping beings of great power, talk of being possessed by some of said beings, the whole Violator incident (and its aftermath), general amorality, none of this is portrayed as being good or right, although the soul eating thing is portrayed as a necessary (or at least unavoidable) part of getting stronger in order to defend humanity.

I did like it, and it is probably less disturbing than NGE apparently got near the end, but this is based on the work that brought you Post Apocalypse Stress Disorder (my nickname for it) and eldritch mecha, so if you take offense at enough of the previously listed things, you should probably give this one a miss.
Update: Last chapter has been published, but not available from the main page.