- During a bad storm that leaves him quaking with fear, Shinji puts a Space Marine model in front of his lantern and is able to sleep soundly, feeling protected by his superhuman guardian. This eventually leads him to create mental constructs of his four favorite models, turning to them for advice and companionship. Years later when the Eva story proper begins and his first connection with Unit 01 is going badly, his mindscape is left as a howling storm...until three words ring out: "THE EMPEROR PROTECTS!"
- Also, he manages to bond with his formerly distant aunt and uncle.
You're not my son...but I think I can love you just the same.
- When he bonds with Rei by giving her a set of Warhammer stuff in Chapter 7. It was the very first time she got a gift...
- "THE EMPEROR PROTECTS!", or anytime Shinji's imaginary friends save him from his self-doubt.
- Some of the Maya-Ritsuko moments (not those kind) are "awwww"-worthy, too.
- There's also the scene between Rei and Shinji in the Alternate Universe omake, which is so cute that it gives Asuka a nosebleed.
- Shinji earning Rei's eternal devotion at the end of the battle with Ramiel. Also insanely awesome, and gives Ritsuko a headache trying to figure out how they managed it.
- Shinji and Asuka's conversation in chapter 36. It starts out with Shinji trying to cheer Asuka up, and it ends up with Shinji growling "You. Are. Mine" in her ear, kissing her, and Asuka tackling him and declaring "And YOU are MINE, Third Child."
- Shinji training Asuka to use her A T Field in chapter 22.