Heartwarming moments in Thousand Shinji:
- When Misato "invites" Shinji move in her apartment he, being an utter jerk, thinks of ways to manipulate the situation in his favor and exploit and use Misato. All of it goes out of the window the next morning when Misato wakes him up and he weeps because no one ever had treated him like a son since his mother's death. Since that moment he started to regard her as his surrogate mother. Which basically means "Touch her, hurt her and you DIE."
- Before the final battle against Ramiel, Rei pecks Shinji's forehead. He touches the place her lips brushed and hurriedly thanks Tzeentch for finally giving him what he desired: a family to love.
- In chapter 4 Shinji meets Asuka and he feels how fragile and vulnerable she is underneath her wrath and passion. He ponders he is finally getting what he had always wished for: he has now a mother (even if she behaves like a Slaaneshi princess) and a sister (even if she is a Nurglette). However Tzeentch has sent him his greatest puzzle. Can he romance a wounded berserker?
- In chapter 5 Shinji talks Asuka into fighting together: he will be by her side fighting while she repays her hurt with death.
- When they sleep together before battling Israfel, Shinji tells Asuka he loves her. When she asks why he questions, "If my answer was anything other than control you would believe me, even if it is the truth?".
- Shinji and Asuka's kiss in the next chapter after Shinji tells he wants to help her freely and readily because he knows she is just like him.
- The fact that Shinji — a disciple of the Chaos God of Manipulation and Trickery — put effort into being honest and truthful as he courted Asuka and always waited until she was ready to give another step further speaks volumes about how much he cared about her.
- In another chapter Shinji and Asuka talk and she asks why he has not suggested so far that they have sex. Shinji replies if they go too fast before she is ready and he hurts her, he would never, ever, forgive himself.
- In that conversation she tells she is afraid of losing him. He replies she will never lose him, and even if he died he would return to her. What if his soul ends up in Heaven? Any place without her would be a hell. Aww.
- After waking up from her coma Asuka realizes he returned. He DID fulfill his promise. And now she also has her mother back, so that she will never be alone again.
- When Rei merges with Adam and Lilith's body and rises she looks like a Nurgle follower (a corpse from someone died long ago). Shinji still calls her "beautiful".
- At the end of the history Shinji, Asuka and Rei have a threesome; Touji and Hikari are reunited; the new Chaos Gods reward their followers, friends and beloved by their faith and friendship; and they turn Pen-Pen in the God Emperor Penguin.
