- Any of The Doctor's Pet the Dog moments toward Shinji, as well as Shinji's slow Character Development into a happier person.
- The revelation that Shinji didn't have any trouble thinking of Rei as a person after finding out what she is, and in fact still had a crush on her and was actually trying to ask the Doctor for advice on how to admit it to her. He no longer has a crush on her, but that's because he found out what else she is.
- The Doctor trying to convince Rei to consider herself her own person. She admits that the prospect of autonomy terrifies her, before the Doctor reassures her. Never has the act of taking a jelly baby meant quite so much.
- Rei, of all people, becomes quite protective of Shinji after finding out that they are, genetically speaking, brother and sisternote (and that the reason Shinji has been avoiding her isn't because he thinks she's a threat, but because he's a bit embarrassed he had a crush on his sister):
- During Episode 11, when Asuka starts going on and on about how she will have justice and Shinji will feel her wrath, Rei hits the emergency stop button, turns to Asuka, then, without displaying any emotion, tells her that if she willingly causes Shinji any physical harm, Rei will kill her. She does promise Asuka that, if it comes to that, her death will be painless. After Rei leaves, Asuka notices that she pressed the emergency stop so hard that it cracked the screen. She did so with one finger.
Heartwarming / Series Thirty and Three Quarters