The following scene with Commander Ikari is really just set-up for the final conflict at the end of the chapter, explaining a little of the physical staging for the events that are planned, and some of how Eve works. It's still vague at this point, because revealing everything here would simply spoil the fun, and be out of character for Ikari-scenes. The real point, however, is that he is setting it up so Rei's will determines the outcome. He's giving her a shot, however minute, which is quite something for him. He is still the sole source and cause of the problems in this chapter, and thus remains the villain of Kenosis. He's just not completely evil. (Mostly... but not completely... *smirk*)
The next scene is very important for the opposite reason. While giving further foundation for the coming events in the large chamber, this section really shows the thought-path Fuyutsuki is going through. It is clear he doesn't like what's going on, and his faith in their work is growing less by the second.
Focusing back with Cirus, he finally heals himself, and starts out. In case it's not clear with the Rei-centric scenes, I always show Cirus' appreciation of her if I can get away with it. Her reaching out to his hand at the end of the last chapter had more effect than she even realized, as always. He never assumes she feels happiness with him, and each time she shows it, it is a fresh and soul-soothing gift. And, again, when it comes to Rei, his 'cold, calculating' side completely collapses, and he's reduced to a 14 year old boy with a crush. Able to pull himself together, he realizes that she would want to know he's on his feet, at least, and wouldn't mind being bothered to learn that. So he sets off.
Kaji has gotten very little page time in actual plot-pertinent events in Kenosis, so I felt a small drive to use him in this final sequence. His seeing Ritsuko after she has, the reader hopefully realizes, just learned about Project 7 from Ikari. Kaji's old detective instincts kick in, and he effectively gets to work immediately after this event, simply behind the scenes and out of sight (reader's included). A detail in this scene that I feel is very important is Ritsuko's emotional reaction to the news. It is clear she is not prepared for this change from the new decorum of Kenosis (compared to the series), and that she doesn't really view the shift positively. From a cold, analytical perspective, this is just me villifying Ikari by making all of his old accomplices appear more heroic. That's true, but the real point is that I saw the opening for such 'redemption' in Fuyutsuki and Ritsuko... not Ikari.
In the series, I found that Shinji was, despite his horrendous flaws, meant to represent a certain 'every boy' facet of the human condition. This was especially apparent to me in the scenes where he's caught in a compromising situation with a girl. The first real interaction with Rei, what he did with Asuka in the movie (which, with where Kenosis cuts in, did still happen), etc. He's that 'proto-pervert' that I think a lot of people assume all men to be. I find that inexcusably evil, personally, and make my point through Cirus. I'll get back to this point in a moment. Cirus surprises Shinji with his arrival in the beginning of this scene. At this point, Shinji basically sees Cirus and Rei as a couple, so is surprised to have them arrive separately. Cirus would never assume anything from Rei, so makes it clear that she is completely free, as she always should be. I do find something very cute in how Rei peeks out fo the water, sees Cirus, and smiles. Their dialogue, and Cirus crouching down to talk to her, is probably one of my favorite moments in the story, accidently so, just because of how well the various details flowed together. Completely dismissing Asuka's previous crush on Cirus seemed inappropriate, so I have her maintain a certain jealousy for his attention. He handles it in good humor, showing his own growth in patience.
Back to the 'proto-pervert' thing. Whereas Shinji has the usual 'furtive glance' response to two beautiful girls in swimming suits, Cirus response is restrained and different. Cirus averts his gaze completely before Rei is even really rising from the water, and this surprises Shinji. As embarrassed as Shinji gets, he's still quite flexible on 'seeing'. The real point is dignity. It's very hard for a man to look in a woman's direction while she's wearing a skin-tight swim-suit (if not a bikini), and still see her as a human being. Cirus would probably have a psychotic episode if he found himself watching Rei in that manner, since he wouldn't inflict that on any woman purposefully. His little exhale of weariness near the end of this section (the difference between his and Shinji's reactions), is actually him showing weariness at his own male nature. Keeping this in mind, the reader might realize that Asuka's blunt rise from the pool and insisting on Cirus' attention only serves to aggravate him further.
This also marks the first time Asuka really understands that Cirus isn't quite normal, or more specifically, he's similar to an Angel himself. This obviously disturbs her, but enough has happened to where she can roll with it rather than snapping. Cirus just responds with his usual dry humor.
Rei's surprise at Cirus pulling the seat out for her always makes me swoon (like most things featuring Ayanami-sama), and this starts what is, effectively, the final battle between Rei and Asuka. The interaction between Shinji and Cirus in front of Rei while Asuka is gone may be a bit confusing because so much isn't said that actually affects their dialogue. The 'distinction' Shinji points out, and that Cirus missed, is thus: Asuka isn't jealous of Rei. She's just jealous for Cirus' attention. I.e. like her mother and the doll. She wasn't really jealous of the doll's qualities, but her mother's focus on it. Rei, explicitly, makes this connection for the reader, but the point would still only fly for a fan of the series.
At this point, both Asuka and Rei are ready to settle this problem between them. It is also the closest Cirus comes to actually physically attacking Asuka for her words. As the argument progresses, it seems Cirus is ready to actually hit Asuka with the big point lingering behind her jealousy all the time... when Rei comes to her defense. Rei's unique manner disarms the situation, and clarifies things for Asuka quite effectively. Cirus reveals he was taking a chance, apologizes, and leaves after Rei. Finally, it seemed to me that the line 'that's good for you' was used to signal Shinji's growing attachment to a given woman, thanks to her resemblance to his mother (most guys look for a woman like their mother in some fashion). Asuka using the line is my 'subtle' (i.e. not at all) signal that she and Shinji are the pair in Kenosis, not Shinji/Rei. Ironically, considering the nature of Kenosis, Cirus and Kaji are very similar characters. I decided it would make sense for the two to be familiar with a 'coded language' for making contact, despite never making arrangements together. So when Cirus is contacted, he knows where to meet Kaji. The meeting itself sets up the final sequence specifically, and brings back Cirus' operator (yes, the one he's spoken with on the phone before), Yachi. Using some character-interaction and referencing un-narrated history between Cirus and Yachi to give the situation more depth, the first part of the chapter ends with Kaji volunteering to replace Cirus should things go awry. Indeed, they are like-minded men.