Reichu: Shinji: "If I can't see it, maybe it can't hurt me!"
Magami No ER: I notice that a lot of the facial expressions in this episode, like this shot, are very humanistic, especially those of Shinji, Misato, and Toji. Another useless but fun inference. :P But seriously, doesn't he look intense?
Incisivis: I'd say it's a combination of "Oh, crap, I can't see it!" and "I'd better keep an eye out before it attacks again!". He's scared, but he's trying to focus.
OMF: I'd say there's also an element of "Well, I did like I was told, so it should be dead, right?"
Reichu: Yeah, there's a bit of anticipation in those eyes.