I think I understand your idea, if you don't mind, I do have to mention- I think Naoma is an issue to the equation.
I mean, I am not opposed to go for a main antagonist, but I think antagonist in this case maybe is not, a villain in the traditional sense.
Naoma is, a piece of garbage, with all due respect to my lovely creation, because I made her that way. She's "chaotic-neutral" in her mind, but really, she's an awful person, doesn't care for her country, her people, and her friends are technically a part of her collection that just happens to still be alive.
I mean, if anything the character with the cleanest moral compass is Alice, which is saying a lot for an assassin.
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I think the religious organization can work, but, how can we work around this to make them, actually an issue.
Kana and Naoma obviously have issues with a religious group against abyss users and necromancers, and I guess Alice is also on their list just for mere connection.
But, what is worse than espionage, warfare and violation of natural laws like death?
I think that is the main question to work on an antagonist.
That or I can sacrifice Naoma and use her as your antagonist if you consider someone who wants, eternal damnation for everyone as a worthy antagonist.
That is what I had in mind I think, but it's just an opinion, to be honest I'm happy to work with anything else you have in mind.