- In spite of everything they've been through and everything they've done to each other, Asuka and Shinji realize that they can't stand to stay apart.
- Shinji and Asuka finally talk about their parent issues and realize that they're Not So Different. And then they hug.
- Asuka disliked Keiko and thought that she shouldn't be an Evangelion pilot (and honestly, she had a point). However, when Keiko says she can't quit because she feels close to her mother for first time in years, Asuka, in spite of herself, feels compassion for her, and reassuringly strokes her hair.
- Nakayima is so surprised by Miko's openness and honestly towards him, that he decides to tell her all about his Dark and Troubled Past, something he hasn't shared with anyone else before.
- Misato knows she can't heal her kids... but she'll do whatever it takes to protect them.
- Rei and Keiko develop a very strong relationship. Before the Final Battle, they had the next exchange:Rei: There is something I need to do. Whether I will see you again, I do not know. To say that I will when I might not would be to make a promise I cannot keep.
Keiko: Promise me anyway. I'll feel better.
Rei: I promise.
- Shinji's increasing understanding of Asuka as a person, also leads him to get an important epiphany about his father, namely that Gendo is also in emotional pain, still deeply haunted by the loss of Yui, and that is why he is so cold towards him. This leads Shinji to discuss the subject of his mother and the nature of loss with Gendo, during which Gendo argues that no one can truly bear the pain of loss and it is better to bury the memories of the past in one's heart lest they drag you down. When Shinji answers that he doesn't believe that to be true, saying that he misses his mother and it is painful to think about her, but he refuses to forget her. Gendo falls silent for a moment as he considers this answer, and then tell sincerely tells Shinji that he might be a stronger man than himself.
- At the very end, where Shinji strokes Asuka's cheek while she's sleeping, so she knows he's always with her.
Heartwarming / Neon Genesis Evangelion: Genocide