Shinji does not return to Misato only because he is afraid that Rei has died and does not want to be in tension after her death. so this is his third day with Kaoru.

Kaoru, lying on the bed, gets up and leans towards Shinji, placing his hand on his shoulder. "What a complex system you have in your brain, huh?” "You hate me, but you feel most comfortable with me.” he yawns and then leans back on the bed. “Whatever, do what you want.”