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One of his favorite things about Kaworu is his spine.
He loves watching the bones lock and shift, feeling the vertebrae underneath his fingers. Kaworu likes being touched there, as well, which works rather well for both of them. He make soft noises that sound to Shinji not unlike those that a kitten would make. Often is the day that the two sit languidly in NERV’s gardens, Shinji trailing his fingers down Kaworu’s spine. He touches it spider – light and whisper – soft, lets himself steep in thoughts he doesn’t normally let himself think about.
And when the tears come, he just rests his head on the part of Kaworu where his spine connects to his head and lets himself cry.
Shinji understands that Kaworu opened himself up to Shinji long ago. It's his own fault for not realising this earlier, because now, with Kaworu making soft contented noises, Shinji wonders how much time he has with Kaworu. He learned long ago that he doesn't generally get much time with the people he trusts, and more often than not it's his fault for their fate. Like Toji's broken body and ruptured spleen, and like Asuka's bomb - heavy silence. Shinji's thoughts are crumpled up, noxious in looks and worse up close. If only he weren't so selfish, so lonely, so irresponsible...
Maybe in a different world, he could be alright and happy. But that world isn't this one and Shinji must cope.