The hair petting may not be the wisest move on Shinji's part, and that thought settles in his mind very subtly the longer this goes on. He doesn't know if he has it in himself to really stop, not when she's still so miserable looking, but he does slowly move his hand down to, instead, rest at her shoulder. Easy, now.

"I was... really scared," he offers, a quiet confession to answer her sentiment, "that I wouldn't see either of you ever again. So this... this much is good."