This confrontation between Ikari and Rei was very much meant to be the final conflict with Rei marching out victoriously believing in her humanity. By the act of adding the second story, the second 'half' of Kenosis, I reduced this scene to an important, but partial step in that direction. She is confident here, but later that confidence is shaken, as is the case with any confidence in any person. Eventually our certainty approaches doubt. It is how we face that doubt that determines a great deal of who we are. To be specific, as I read the scene now, it feels rushed to me. I wanted Ikari to say more to Rei, especially as she draws herself in, feeling attacked, but I couldn't come up with more phrases or facts to draw it out more. However, Rei's confidence is clear. She is not submitting to Ikari this time, right away she is apt to stand up and defend her action, only conceding to the sincere danger of the Angels if she's too chaotic on the field. (Compared to Shinji, the idea of Rei, even with her affection for Cirus, being a danger of spazzing in battle is... well... laughable.) And, of course, Rei being so strong-willed is quite shocking, even to the irrassible Gendo. The finish of the scene is indeed abrupt. Originally, I intended for the impression of Yui to end Gendo's desire to control Rei for the finish of the original story. He rethinks that conclusion later, though I never specifically narrate that fact. I let the fact that Gendo is so well known for being a controlling jerk hide his moment of humanity here when compared to the latter story.
Beyond establishing that Cirus is 'up and about', the next section has little purpose. I always use such chances for character-interaction, to keep the story 'real'. Cirus would never 'chase down' Rei... he rush to her, of course... *chuckles*. And I couldn't resist making Misato sound like an old, wisened woman in the ways of the world.
With the return to Gendo, it seems I'm just trying to contradict my own story, but, in fact, I left this scene in because of the very end. Koso's challenge to understand his point in Gendo's own way is the key opening I can rely upon for Gendo's future reversion to controlling Rei. Gendo only thinks he has the answers here. And it may seem I'm spoiling a great deal of the later story, but in this commentary, discussing the weaknesses in connecting the plot together is a key feature, and Gendo's capacity for selfishness is hardly surprising, especially in regard to Rei.
Honestly, the scene with Asuka, Shinji, and Cirus in the wall way was little more than keeping Shinji and Asuka in the story as major characters. I was sorely tempted to just... leave them out. So with the usual dry humor, reparte, and so on, I let them play out their little interaction, and have Cirus head off for the next scene...
The 'comic book super-villain' narration comment is probably my favorite personal quote of the entire story. It's just so... me. And, heck, I think it works for the humor of the scene. Not wanting to make Misato seem totally manipulative, the seriousness of the last battle makes her decide to give the kids a pleasant night off together. Proving her sincerity with Cirus also lets me show an aspect of Cirus' personality that isn't quite expressly narrated in Kenosis. Treat Cirus fairly, and he'll reciprocate. Since Misato was so honest, he responds far more directly than usual, though still keeping certain private facts to himself. The final sentence was never meant to spoil the humor of the story, but since it ends the part it seems a bit dark. Really, Cirus is just reflecting on how hard it is to balance life's realities with a healthy amount of fun.