The theme is provided by the answer to 58-Across: Chaos… or a hint to the contents of 17-, 28-, 34-, and 43-Across. Answer: General disarray.
The four theme answers include the word “general,” but the letters are in disarray, i.e., not in order.
17A. Many a Manhattan Project worker = Nuclear engineer
28A. Growth on wet rocks or the surface of stagnant water = Green algae
34A. What a coiled spring or charged battery has, in physics = Potential energy
43A. Targeted area? = Rifle range
I actually filled in the four theme answers first but had no idea what the theme was until I was able to fill in 58-Across. I ran into a problem there. I got “general” and when I got “dis” –both of which I knew were correct based on the fills surrounding them – I figured, “Aha!” — “chaos” = “disorder.” And thus, the theme became clear. But — and it was a big BUT — “order” didn’t work with regard to completing that part of the grid (and, thereby, finishing the puzzle). So, I erased it and after filling in a few other answers, I realized that the correct word was “disarray.” After that, completing the rest proved easy.
This is the last Thursday puzzle of 2013.