After Shinji and Asuka have been in the past for a few days, Asuka asks Shinji to play their daughter's song on his cello.
Asuka: Please... Please play her – her happy song! I need to hear it again!
Shinji: I'm sorry. I- I don't think I can. It is supposed to be a happy song after all. But now it wouldn't bring anyone happiness – because it was hers.
Asuka: It would ease my sadness! I have nothing else from her! I don't have photos of her, I don't have one of her drawings, I don't have Kiko, I- I don't have... *sob* Please. That song... that song is all there's left from her.
Shinji: I'm sorry.
All the tearing up can be summed up in one word: "Mama...?"
When Shinji and Misato try to stop Ritsuko from destroying the Dummy System, Rei unexpectedly shows up and picks up Ritsuko's remote. After explaining why her spare bodies cannot be considered as human beings due to their lack of a soul — and commenting somberly about how, unlike her, they are spared from the burden of human feelings —, she then proceeds to destroy them herself, to the surprise of everyone present.
When Shinji gets absorbed into his EVA in chapter 5:
And while the berserk monster slashed out at its opponent to kill it and to devour its remains, annexing a power that went beyond anything it possessed; while a young woman vomited and her colleagues just stared in shock; while two conspirators pondered about the consequences of this beginning and while another man just seemed to water his patch of melons in the distance, a teenage girl wept silently for a loss she couldn't even see, but could only feel in her heart.