Close-up of Shinji. He is looking at Ritsuko
When he turns his eyes to look straight in front of him, he hears Rei’s line and turns his eyes towards Rei
SHINJI (MONOTONE):“Meaning we’re in trouble, huh.”
REI (OFF - RIGHT):“I...”
Kendrix: He looks serious and stoic here, or at least tries to. This is definitely not the cosmic plaything we saw in the past episodes. The afore mentioned change is beginning.
Note how Rei asks her question in this exact moment, when he is told that everything is resting on his shoulders, as if she wanted to remind Shinji that she's still there, but couldn't think of the words to do so.
It makes sense, I mean, she was certainly paying attention when Ritsuko assigned her the job of the defender earlier.