[She followed his conversations with the others, reading without contributing, and noticed his usual investigative approach... now, seeing just how upset he is to have Junko haunting him (and who could blame him?), it makes sense to her]

Were you anticipating that she might appear to you, then? You must've been hoping to avoid it.

[What can she even say to comfort him? Only the measliest consolation comes to mind:]

Now that it's come to pass, at least the anticipation is over.