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I think that having him struggle to reconcile his religion with his life experience, as you said, will really help with the issues you are concerned about. It humanizes the religious character and ...
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#3: Attribution notice added
Source: https://writers.stackexchange.com/a/46878 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
I think that having him struggle to reconcile his religion with his life experience, as you said, will really help with the issues you are concerned about. It humanizes the religious character and shows that they aren't so judgmental and steadfast as other books and movies would have the public believe. A huge part of religion is an endless struggle. I think your character will be relatable to both religious and nonreligious readers for this reason. I think it is worthwhile to spend time showing his inner (or outer) deliberations about his religion and times of doubt for him. Maybe he could even leave the religion for a bit. Just remember to keep it sincere—there are far too many Christian movies where a character "leaves the religion" but there's no real impact to it because the movie is so preachy. But as long as you keep the religion restricted to that character and out of the rest of the book, you should have no trouble with this. This book sounds really cool and I'd love to read it. I'm especially curious how this character will reconcile his religious beliefs with magic. I also like writing supernatural stories with religious elements, but fitting both together is nearly impossible as you have mentioned in your post.