Contains spoilers for this episode and earlier episodes.
Misato discovers that Shinji has left the apartment after several days away from school. His classmates bring missed assignments, but she conceals his disappearance by saying he is training. Shinji spends his time riding trains, listening to the same music and watching a late-night film before wandering into the countryside. He encounters Kensuke playing at being a soldier and accepts an invitation to camp with him. Their conversation gives Shinji a different view of Toji, who regrets hitting him. Kensuke's enthusiasm for piloting also meets an awkward limit when the boys discover that neither of them has a mother at home.
Nerv agents collect Shinji the following morning and return him to headquarters. Misato asks whether he wants to pilot again, but their argument ends with his resignation. Gendo accepts the decision and prepares to use Rei instead. At the station, Toji apologizes and insists that Shinji hit him back to settle their earlier fight. He understands why Shinji wants to leave, even though losing the city's defender may force their families away too. Shinji condemns himself rather than accepting that kindness. Misato, recognizing how badly he wanted a home, rushes to the station. She finds that he has not boarded the train, and they greet each other as family.