I need to add some scenes, particularly with the villain and relating to his evil plots, but before that I'm making the more subtle changes, the ones that alter the way characters and their relationships are. So, in the original version, two characters had been childhood friends and, in their teenage years, lovers. In order to point up that one character worries about his sexuality (he's bi), I decided that his friend had been much less emotionally involved in their teenage affair than he had been, and that they both knew it, but didn't ever talk about it. At the same time, the friend is charismatic and physically demonstrative, so that's now an added small pain, a constant reminder that his physicality is often casual.
Also, I'm trimming down the numbers of the background soldier characters and giving them a tad more personality, not so much that the reader really has to keep track of them, but enough so she can if she wants to. And I'm giving them a bit more toughness overall, more trash talk, more reason for the characters with alternate sexualities to feel nervous.
I still have to decide some details about the evil scientist plot, but that's coming together, as well.