[Haruhi looks very confused for a moment when Shinji starts talking about NERV. It takes her a moment to process Shinji's fear in context of what she just saw. He must think this is just a repeat of whatever that was. Her confused expression shifts into an understanding one and she lets out a small sigh.]

Ikari-san, this isn't a project. Everything I know about NERV is because we came to rescue you. I still don't know why we have personas but it doesn't have anything to do with NERV.

[She looks away from him briefly to give him privacy to process this information.]

You don't have to talk about it if you don't want to, but it does seem like your experiences might answer a lot of questions we've had for the past year.