Kaworu and Shinji (Relationship)

Though fans have speculated on what kind of relationship Shinji had with Kaworu it is at least clear that Kaworu represented a sort of idealized friend-figure to Shinji, possibly more than that, granting his wish for someone to understand him, treat him well. Developer commentary mentions the subtext between the two and at one point a kissing scene was planned, but eventually cut. Shinji also found himself confessing his own emotions to Kaworu, talking about things he hadn’t had with anyone else. Kaworu came to Shinji in his darkest hour and gave Shinji the kindness the Third Child so desperately sought in others, only to feel horribly betrayed and hurt when it turned out Kaworu was the final Angel.

This, paired with the fact that Shinji had killed what he saw as a human being, was part of what drove Shinji into his state of absolute despair in Episode 25', in which he declared that he felt unworthy even of the piloting which had consumed his identity, thinking that if all he did was hurt and kill others, it was better to do nothing. By that, though, he may have condemned Asuka, who was fighting against the Mass Production Evangelions, to death.