First of all, I want to begin by saying that Luann Reed-Siegel has done an absolutely brilliant job in copyediting a very difficult manuscript.
The difficulty of the manuscript is only partly a matter of its sloppy author; a problem throughout this series so far has been how to mix the more conventional Chicago style with the peculiar style variously called Federal, Federal Security, and Defense/Security that is used within the American federal government. Because public servants in the United States are required to be extremely mindful of the requirements of the Constitution (which I hope most of you will see has a great deal to do with the story and how things unfold), it has long been customary in Federal documents to capitalize nouns when they refer to Federal and Constitutional functions (as I just did there) and not when they refer to other matters, in effect supplying tiny warnings to public officials when they are in areas where they may have important legal responsibilities.
Thus the President is the Commander in Chief of the Armed Forces and the Vice President presides over the Senate, but the president and vice president sometimes order a pizza in and spend the evening watching the Three Stooges (who, curiously, have no Federal function).
Similarly, the United States has an army and a navy but the Constitution governs the relationship between the rest of the government and the Army and Navy. This can result in apparently inconsistent, yet correct, capitalization on the same page or within a single sentence, and I just wanted it clearly stated that Luann Reed-Siegel has in fact done an excellent job with it, and that since I reviewed and approved it, any errors remaining are entirely my fault.