Shinji; the third children
In contrast to their initial meeting in the anime, the manga version of Kaworu had little praise for Ikari Shinji's piloting career. Much like in the anime, Shinji is first aware of Kaworu by the song, Ode to Joy. Instead of humming it, like he did in the anime, Kaworu was playing the piece (unknown by name to him) on a piano in the remains of a neighborhood destroyed in the previous battle with the Angels.
They chat aimlessly until Kaworu killed the kitten Shinji had found, justifying the act because he was removing the suffering it otherwise would have gone through by starving to death. Needless to say, Shinji was left aghast, remembering the only other time someone made him feel this way was the old Ayanami Rei. Unlike the anime version, Kaworu and Shinji's relationship started off rather turbulent, and both Kaworu's view on the kitten's life and the confusion he brought to Shinji positioned the theme for the rest of their relationship.
If we both left, who else would come? He'd slowly starve to death on his own. And if that's all there is—then what I do is kinder. Nagisa Kaworu, Stage 57
After identifying himself as the Fifth Children, Kaworu proceeded to follow Shinji around, making Shinji his unwilling tour guide. And as Kaworu was further intrigued by Shinji's illogical responses, Shinji was further disturbed by Kaworu's seemingly uncaring words. The more he saw of Shinji, the more Kaworu was fascinated by Shinji's emotions, and his vast range of reactions.
They're strange—humans. They're so curious for the state of things outside themselves. They get maddened and flustered... Angry and frantic for the sake of others. They brood and they worry over them. It's fascinating to watch. Nagisa Kaworu, Stage 62
Throughout their relationship, Kaworu seemed to irritate Shinji to no end. In one instance, Kaworu barged naked into Shinji's shower stall, simply because his stall had insufficient soap. This produced one of their more comical scenes, in which their bodies' proximity are closer than the anime version of the bath scene, albeit less friendly. Shinji just can't get used to Kaworu's odd behavior, and even told him straight out that he did not like Kaworu.
I have to confess I initially did not like how Kaworu was portrayed, since I was used to the much more gentle and comforting personality he provided in the anime, but after reading the manga chapters the first time around, I thought about it more, and the the discomfort I felt was due to the misguided notion that any change was too much change, rather than disagreeing with the actual content. At first I didn't like how Kaworu and Shinji lacked a closeness that was in the anime, and how Kaworu did not act as a source of comfort for Shinji, who was reeling from a number of personal losses in his life. After getting over my initial reservations, I have to admit the manga portrayal felt more "real," in the sense that Kaworu was more than just a vehicle for Shinji's comfort; he was a separate character with his own goals and desires.
Sadamoto also took some interesting liberties with the way he portrayed the relationship between them. Instead of purposely touching Shinji to comfort, many of Kaworu's physical moves on Shinji was a by-product of something else. The shower scene, for example, arose due to Kaworu having less soap in his stall, and his lack of social sense and him just barging into Shinji's, with no regard for personal space or modesty over nudity. And when they "kiss," it's due to Shinji hyperventing, and Kaworu using his own mouth to cover Shinji's, and then gleefully realizing that it didn't have to be a paper bag. Later, due to the battle with Armisael, in which the Angel passed some of Ayanami Rei's emotions into Kaworu, one of my favorite lines by Kaworu was spoken, after the "kiss."
How does it feel when a person comes to like another person? Wanting to touch them. Wanting to kiss them. Not wanting to lose them. What does it feel like? [...] A tepid, sticky, disgusting feeling that seemed to slowly constrict my chest... Is that love? Nagisa Kaworu, Stage 67
After that alarming pronouncement, Kaworu asks Shinji directly, "If you came to love me, I wonder how that would feel?" To which Shinji naively shouted, "Guys don't love other guys!" Despite the words they exchange, make no mistake, Kaworu was not declaring his love for Shinji. These human emotions fascinate Kaworu, and the illogical way Shinji behaves draws in Kaworu, as he doesn't understand that sort of behavior himself. During his battle with Armisael, Kaworu received remnants of Ayanami Rei's feelings for Shinji, and it was this feeling that was confusing Kaworu. He experienced part of Rei's love for Shinji, and the sensations they brought were foreign to Kaworu. His fascination with these feelings was what drew him to Shinji, though Shinji was mostly repulsed by Kaworu at this point—not remotely close to love, as he was in the anime version.
Shinji only sought Kaworu out because Kaworu was the one person who was unaffected by the possibility that Rei could have died from their battle with Armisael. Kaworu's apathy was a distraction, a shield for Shinji to justify running away from having to face reality. And this was in line with how Shinji reacted in general to things he did not like. When Kaworu made him feel uncomfortable, like in the shower, or when he declared he wanted Shinji to love him, Shinji chose to ran away rather than face the problem. After the run in with Kaworu in the showers, he sought out Rei for support and affection. When Kaworu questioned Shinji on love, Shinji escaped having to answer when Misato called, letting him know that Rei indeed survived the explosion, much to everyone's disbelief. Though in reality the Ayanami Rei that Shinji had grown to know actually died in that battle, and the Rei that "survived" was really another clone, the third Rei to exist in the story.
After the battle, Rei's self-destruction of Unit-00 to defeat the Angel caused a large surface area of damage, and most of Shinji's friends left the city. Despite being virtually alone, Shinji still refused Kaworu's offer of friendship. This finally caused Kaworu to break his cool demeanor and display more human emotions. As Shinji despaired that he was better off never having friends if he was going to suffer losing them in the end, Kaworu only cared to hear what Shinji thought of him. In this instance, he displayed the most childish aspect of his personality—not at all like the anime version, which portrayed him as caring and supportive, empathetic to Shinji's situation. His manga persona was much more selfish and detached. He only wanted to monopolize Shinji in a way that satisfied his own vanity. He wanted Shinji to care for him, even though he did not care for Shinji. In a way, this made Kaworu very human. Though he lacked other qualities due to the way he was raised by SEELE, Kaworu possessed one basic drive all humans have: the need for love and acceptance.
After this rejection, Kaworu finally stepped back into his original role as an agent for the committee, resuming his duty and speaking with SEELE once again. To carry out their plan, Kaworu finally revealed his true identity as Tabris, the last of the Angels. From this point on, Kaworu masked any desire from his face, and accepted that time had come for him to act as his destiny intended. He took Evangelion Unit-02, and proceeded to descend through Central Dogma, under NERV headquarters. When Shinji was sent in pursuit, inside Unit-01, his fears of attachment was confirmed. Why did Kaworu act so friendly towards him if he was only going to be an enemy in the end?
After explaining why he could control Unit-02 outside of its entry plug, Kaworu taunted Shinji with the fact that Shinji had never liked him anyway, so fighting him should not be a problem. They fight and Kaworu explained the origins of the A.T. Fields. The two Evas battle until they reach Terminal Dogma. As Kaworu contemplated the fate of the Lilim, he also revealed the truth about Third Impact.
Even if Third Impact occurs, people will not simply perish. They will be reborn in a new form, merged into one as a single life form. [...] Wars and conflicts, the suffering and sadness of losing people, you will be freed from all of these. Nagisa Kaworu, Stage 73
Seeing Shinji's continued rejection of Third Impact, Kaworu measured his fate and he chose to die by his own will, as his fate was to cease in existence regardless if Third Impact occured. Kaworu then made his final request to Shinji, "What I would like is to to die by your hands. [...] And if you ever felt anything for me, you will grant it." After dealing with any remaining qualms, Shinji finally complied, face full of confusion and distress, admitting that he will never be able to forget Kaworu. Despites his best efforts to the contrary, Shinji had indeed grown attached to Kaworu in the short time he had known him, developing a sense of rapport. Kaworu was always around, and even though he had warned himself against attachment to another person, Shinji still could not help but have some feelings for Kaworu.
Their story comes full circle, and Shinji's act of killing Kaworu is reimagined on an empty field, much like where they met. The scene plays out as if mentally inside Shinji's head, almost like it's his way to cope with the magnitude of what he is about to do. It is Shinji who chokes the life out of Kaworu, strangling him with his bare hands, releasing Kaworu from further suffering and giving him the same "kindness" Kaworu had shown the helpless kitten Shinji found when they first met.