Detective Diary gives even less of a damn than Angelic Days does about explaining what the heck is going on: having to cobble together an ending due to cancellation is no excuse for this when Campus Apocalypse did such a great job handling its plot threads and having stuff make sense when it was in the same situation. There are hints that parts of the original series' worldbuilding are still true in this 'verse, there's something about the Road to Adam, but it doesn't get followed up on.
The manga's official pairing is Shinji crushing on Rei.
This is a standard missing scene: I might make an attempt to make the ending make sense at some point, but since I've made a habit of writing things exploring Kaworu's character in different Eva versions, the point of this fic is to address his early opinion of Shinji.
"He's weak and useless," Kaworu said, arms folded. "He can't fight and he didn't summon his Eva. I don't see why we have to play Gendo's games for his son's benefit."
"He's the one that's paying for all this," Kaji reminded him, but that wasn't what this was about. Kaworu normally didn't mind the games: it wasn't like he had anything better to do, and the former lab rat enjoyed human company. The company of humans that treated him like he was a human.
"Even if he insists that you do things with his son, do you have to let him live with us?" and it gave Kaji Asuka flashbacks, really it did.
"Kaworu," he said, "we're not replacing you." They weren't going to throw him out, leave him with nowhere to go, or start ignoring him just because Gendo Ikari sent them over to Japan to make contact with Shinji.
"I know that. He can't replace me." Not when Shinji was useless. "You're only letting him in because you were ordered to. For the money."
He winced. Oh. So that was what this was about.
It was Misato that leaned towards Kaworu now. "I didn't bring Pen Pen home from the lab where he was made because someone paid me to do it, and I asked you if you wanted to come live with me before anyone offered me a stipend, remember?"
Was he afraid that he'd been tricked, the way they were supposed to trick Shinji on Gendo's orders? That Kaji and Misato didn't care about him any more than they did about Shinji? And the worrying thing, the thing that would make it hard to disprove that idea, was that it was more than a little true.
Asuka, Kaworu, and now Shinji: they were kids that were caught up in this mess with the Evas and the Road to Adam. Gendo's faction might have brought down SEELE, but then he'd absconded with a hell of a lot of money and given only a few people invitations to join him. Was the relatively-straightforward Misato only included because where she went, Kaworu went, and Gendo needed his Eva?
Since Asuka was going, Kaji had to, to keep an eye on her. Saying they needed her to save the world; of course Asuka couldn't say no to that.
Then they arrived in Japan, the girls getting set up early to infiltrate Shinji's class, and their orders were to playact. To pretend to be a detective agency. To pretend they needed to find the Evas, even though Kaji was damn sure that Gendo had the five the world knew about and the two they didn't in his possession.
The stories, the lies, were so damn juvenile: did Gendo think Shinji was five? Stealing a plot element from Ouran High School Host Club? (Kaji blamed him recognizing it on Rei.) Kaji and Misato had a lot of practice acting in the kind of situation where a slip-up would get them shot, but Kaworu, Kaji thought, looking up at the office ceiling, hadn't really had the chance to absorb a lot of pop culture. Heck, this might be the first time he played something that wasn't poker with Kaji and Misato. So he had no idea how ridiculous this all was, he was just picking up on hints that Gendo was being ridiculous, was screwing around with someone and it might be all of them, not just Shinji.
The most likely secondary target, Kaji realized, was Kaworu. The boy (the experiment, who might be the Road to Adam) was childlike in a lot of ways. He hadn't learned tact, although he was an eager student of consideration, things like bringing his caretakers ice and other requested hangover remedies. Was Gendo worried that Kaworu would refrain from helping Gendo, the way he'd refused to take part in SEELE's ritual, unless he kept the boy entertained enough to follow along to see what happened? Was it only Shinji that was supposed to get too caught up in this ridiculous game of detectives and robbers to have a chance to get a close look at what was going on under the hood?
Rei was Gendo's, but Kaworu was raised by SEELE's cult: he thought evolution was just a local mythology and everyone knew that life really came from the Seven Seeds sown by the First Ancestral Race. Secrets Kaji'd had to risk his life to get his hands on, and Kaworu thought they were common knowledge because for almost his entire life, he'd been in a place where they were.
Kaworu wasn't responding to Misato's attempts at reassuring words, unless you counted the way he'd turned towards her a little, all the little hints that he was soaking up those words, the suggestion that he was wanted for himself instead of what he could potentially do because he possibly wasn't human like the desert soaking up spring rain.
Aww. Would you look at that. He was smiling.
A real smile, not the smirk he generally tended to have when the puny humans amused him. Not that Kaji could blame him: his entire sample pool for humanity for most of his life was SEELE's crazy cultists. 'You're a bunch of loonies' was the sane and accurate response to those people, and maybe he and Misato were enough alike (he was a spy, she used to be Special Forces) that they were both prone to be a little crazy and inclined to pranking off duty.
He liked them, he really did. A human with all the powers of not just an Eva, but the gems that created them based off a human host's wishes, their ideal selves. And they were the closest thing he had to a family. He'd walk through fire for them and wouldn't think anything of it: Kaji remembered the time he'd thrown himself in front of a bullet for Misato, how amazed he was when she asked if he was okay, when she berated him for it and kept doing it even after he told her that he wasn't in danger from bullets, she was the one who was in danger if they were going to be talking about people who were younger or weaker doing stupidly risky things.
Misato and Kaji were really the last people on earth who should be allowed to be parents, but they were the only parents Kaworu was willing to acknowledge (thank whatever they won, thank whatever SEELE hadn't, because the world they wanted to create…).
Now they wanted to take in another kid. They'd be paying attention to him: that was the job.
Kaworu was reacting like a formerly-only-child who had just been introduced to the new baby, and Shinji hadn't exactly come out of that scene smelling like roses.
"He was living alone," Misato says, playing her trump card. "I'm thinking that he can stay in my apartment with you, and I'll stay with Kaji for the duration of this mission."
Kaji might have thought that was a mistake, except it looked like Kaworu not wanting Shinji trying to horn in on his parental figures beat out the odds of Kaworu taking that as Misato leaving him because of Shinji. He was used to Misato spending nights at Kaji's place. Back when they were in Germany, Asuka would generally spend those nights at Misato's. It gave Asuka some supervision she couldn't browbeat into doing whatever she wanted like a normal babysitter, and Kaworu didn't like to be alone.
He was glad enough to have someone there that he'd started to tolerate Asuka after that week he'd had to stay with Kaji and Asuka when Misato was off on that mission taking down a cell, the one that had the Vice-Commander kidnapped. Hey, at least Kaji doing it for them meant they could finally track them to their nest…
Anyway, Shinji was an ordinary enough kid: he didn't have being impossible to live with raised to an art form the way Asuka did. Living with Asuka was more emotionally draining than being around SEELE members and not killing them: the girl had issues and sharp edges.
Or maybe it was some genius strategy: Asuka'd gotten sick enough of him taking her comments as some form of affection that she mostly started holding them back.
Either way, if he could handle Asuka, he could handle Shinji, Kaji thought, and tried to shut up the part of his mind that remembered that Shinji was Yui and Gendo Ikari's son, and the reason he was still pulling a paycheck from the UN as well was that it might not just be SEELE that was out to end the world.
This manga's Kaworu is more manga!Kaworu than anime!Kaworu, a manga Kaworu who has had a foster family for a few years but still has no tact. The fact his influences (other than possibly Gendo and SEELE) are Kaji and Misato probably had a lot to do with that. Given how he handles Shinji's fever, I'm certain he nursed them through a few hangovers and thinks they are very silly people but much better than SEELE.
Anime!Kaworu's loyalty is to Shinji. DD!Kaworu's is to Kaji, although by the end he's added Shinji to the list of people he considers 'home'/his family.
Kaworu says the thing about Eva's explanation for humans existing on earth (aliens did it) being much more credible than evolution, which was hilarious and says a few things about his backstory in the DD 'verse (SEELE is a crazy death cult).
He also protects Shinji from some glass, and Shinji being worried about him afterwards is one of the things that make Kaworu gradually realize that maybe Shinji doesn't suck.