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 Possibly closer, as The Doctor notes that their DNA match is close enough that a "X-chromosomal clone's just about as likely..."(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 a 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.