Well, I wouldn't worry too much about missing secrets, honestly. I try not to include anything in the game that I don't think is worth your time, but I also don't want players to feel like they have to 100% the game either. Plus, I do think there is meaning in some things being hidden.
Still, I also know how powerful a driver curiosity can be, so if you do feel stuck and want the answer I'll put it at the end of the comment. (Hopefully spaced enough to be beyond the "Read More" dropdown.)
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The current major "route" splits are based on said optional character being 1) Not recruited, 2) Recruited, or 3) Dead.
There are smaller differences in and between routes, as some other actions are tracked, and then of course there's the side-quest plotline, but those are the current conditions for the major "route" splits.