There's no way she could have known that they wouldn't end up in the right place, but Shinji can still see where her worries are coming from to some degree. He can sympathize, his own fears that he was stewing in earlier aren't dissimilar, after all.

But that little apology, that sad plea, it's really testing the limit of how capable he is of keeping himself together right now. He clenches his jaw briefly, like it will keep any sorrow or fear or dread from escaping his mouth, before answering her with a strained, "We'll be okay." They're here, together, like Kaito's said. She can trust him, right? "All three of us, we... we can still protect each other."