Seems I’m a little late to the party on this. At least I have some info to work with here, so I’ll do my best.
Reading through what you have described, it sounds like the only thing standing in the way of the bad people (henceforth referred to as the Bads) are the Christian Sons of Liberty family (henceforth yada yada the Family). And only that family, which is why the virus was made to wipe them from the map. This can be an engaging plot, with a couple things to think about.
Why is the Family the only ones left who follow teachings that differ from the Bads’ way? Were other families and their teachings erased already? What specifically are the teachings that people accepted from the Bads, that prevent liberty and Christianity and arms bearing (I’m assuming that this becomes a large point in the story, as it was the solution for an economic crash)
You had said that this is going to be a thriller/mystery novel. There is certainly an excellent framework for it set up, and many of the elements can lend themselves nicely to it. I think that it might be difficult to work everything into a book and still keep a mystery feel. Were you planning on using something closer to a Bond thriller style, where a nefarious plot is uncovered kinda quickly and hijinks are used to confront the evil-doers? I know you had mentioned you wanted to split it into two books, the first being discovery and the second being reaction. Even just putting all this into the first book might make things feel forced or rushed. Perhaps save some of the “big juicy bits” for the second book. Just a thought.
I’ll be interested to follow how your project goes, and where you decide to take some of these plot threads. If you’re careful, you could have an engaging plot with social commentary about our post-COVID world and what the two political parties are doing to “win their people” over. I assume that these are the things you intend the reader to think about as the things that the Family hold as values are thought of as “belonging to one political party in America.”
"Only a Sith deals in absolutes"