Shinji keeps his eyes averted from Rei’s gaze throughout
REI:“We leave in sixty minutes.”
SHINJI:“Do I... to pilot that thing again?”
REI:“Yes, you do.”
Shinji buries his face in his knees
He spills words out to comfort himself without thinking.
SHINJI:“I don’t…want to.
Ayanami, you’re only saying that because you haven’t had any scary experiences piloting that thing.
I don’t want to – go through something like that ever again.”
REI (OFF):“Then sleep.”
Shinji responds to that line
He lifts his head a little, opens his eyes and looks at Rei (Shinji was certain she would be sympathetic, so from his point of view, Rei’s words were completely unexpected…)
SHINJI (Back -surprised):“What do you mean ‘sleep’…?”
thewayneiac: The description of Shinji's reaction is unsusally detailed. The writers must have felt it vital for the animators to get this cut exactly right.