Rei turns around and faces the camera.
Shinji is reflected in the extreme close-up of her eye.
Kendrix: Maybe his mention of "smiling" (something she had only done for Gendo until this point) made her think of his father. Whatever the exact reason may be, Rei didn't realize the similarity of this situation and the activation experiment until now, which is why she is so visibly shocked. Note that she's already slightly blushing at this point.