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Shinji is horrified that he will have to eat Misato's food again.
In this fic, we learn that Kaji was the one who taught Misato to Drive, much to Shinji's horror.
Shinji slaying Samshel and then asking "Anyone for fried squid?"
Hikari and Touji's sister chewing Touji and Kensuke out after they leave the shelter during a battle.
"I need to change the logo on my NERV patch to 'Asuka is angry with me, all is right with the world'" ~Shinji shortly after reuniting with Asuka.
Shinji's reaction when Asuka and Rei were apparently bonding.
Kaji and Shinji buying Misato a book titled "Parenting for Dummies", and Shinji joking the bookstore had ran out of "Parenting for Guardians of Temperamental Germans" to Asuka's face.
Rei -Rei!- shouting to Kensuke.
Kaji gives Shinji a picture of Gendo holding a gun in one hand, an adorable kitten in the other, and a caption reading:
PILOT THE EVANGELION!
Or the kitten gets it.
Shinji waves back to Chihiro, the hottest girl in school (second after Asuka arrives), who has expressed an interest in him. Shinji then thinks that "thanks to his limited understanding of women, this could be taken to mean anything from 'hi there' to 'yes, I would like to marry you'."
Shinji compares the thought of Asuka and his father facing off against each other to watching someone play with the arming codes to N2 bombs...and considers the latter to be safer.
When Shinji is found after vanishing from the hospital without warning, Misato storms off to meet him. Aoba mutters he would like she did welcome him personally, and Hyuga replies he does not think he would like the welcome that Shinji is going to get. Then Shinji finds himself in a Marshmallow Hell. Misato nearly suffocates him to death, but he thought it was not abadway to die.
Misato catches Asuka tiptoeing out of Shinji's room at the morning, and Asuka has to explain that it is Not What It Looks Like.
"It had taken some fast talking in the living room and not a little angry indignation to convince Misato that nothing untoward had happened between her and Shinji last night."
"And that she did have a good reason to be sleeping in Shinji's bedroom."
"In his bed."
"With him in said bed, at the same time."
"Not that in her opinion it was any of Misato's business what she and Shinji chose to do -or not do- together"
Shinji compliments Asuka over breakfast and she feels so awkward that she leaves the room to hide it. Shinji thinks he's screwed up and angered her somehow... then Pen-Pen walks over and seems to inquire what happened...
"Wark wark, wark?" the genetically engineered penguin inquired, moving over to join him.
"It's simple" Shinji said to the Penguin, suddenly feeling dangerously whimsical, leaning in and dropping his voice to a conspiratorial whisper. "See, I'm actually a time traveler from the future who's come back to stop my Father and/or SEELE from kicking off Third Impact. During the pre-game entertainment to the main event last time, I managed to utterly betray Asuka and abandon her when she needed me the most, despite the fact that I thought I had fallen in love with her and thought I'd do anything for her, up to and including dying… so I feel a little guilty right now whenever I look at her. But don't tell anyone, it's a secret" he finished with an admonishing look before he rocked to his knees and started to gather the plates.
The genetically engineered penguin stared at his back for several long, long seconds before continuing into the kitchen, retrieving a can from Misato's stash, stopping in consideration, retrieving a second, and retreating into his fridge.
"Yeah" Shinji muttered as he stacked the plates in the dishwasher. "That's about what I thought you'd say".
A moment that is both funny and touching, in chapter 5: upon getting ready to sleep in Misato's flat for the first time, Shinji sadly realises just how much he misses Asuka and that he has to wait four months for her arrival. He then suddenly hears Asuka's voice in his head affectionately scolding him to not "mope around" like the old him and orders him to go to bed, making him do a Double Take that she hadn't actually materialised in the flat.