OK, that explains the mechanics.
Now we just need to figure out what the kidnapping means. It creeped me out a bit. With all the talk about AIs in Chuck’s journal, I was half expecting the game to go the “pod people” route. I suspected Reyes had been replaced by an AI (although it was weird that I could still control him), and that one of the next goals was going to be to figure out where the real Reyes was being held, free him, and expose the impostor.
Perhaps I missed something, but to me it seemed like the kidnapping was something totally random that had no bearing whatsoever on the story. Perhaps it’s supposed to be an illustration of the “resets” Chuck speaks about in his second journal? The townspeople kidnap and kill one of the feds, but the outside world intervenes and resets Reyes, who then wakes up elsewhere and assumes he simply blacked out?
Any other theories?