after the battle against bardiel, where the pilot of unit 03, toji is killed, he calls kaji and tells him to bring shinji to him. gendo reads off the list of criminal charges, acquired by shinji who asks his father if he has nothing to say to him, which gendo corresponds, causing shinji to respond by trying to punch him. while held by kaji, shinji begins to scream at his father, telling him that he never wants to see him again. gendo's response to this is the same as in the anime, to have shinji removed from nerv's records. when zeruel attacks, after rei fails to activate unit 01, he heads down to the cage to try to get the dummy system to work, which proves to be futile. gendo, in his first act of distress, frantically asks why unit 01 (and by extension, yui) is rejecting him, to which shinji's picture appears on the screens, genuinely surprising gendo, which is only furthered by his son's reappearance at the cage.