"I get to make that choice, not you." Makoto can't help but assert back.

His face falls into something of shock when Ren mentions the terrible things that would have happened to him if he didn't obey. "You- you realize that you're acting like you had a choice when the alternative was that." He's not worried about the apology for Shinji's death when Ren is admitting to a total lack of agency in his situation.