Contains spoilers for this episode and earlier episodes.
Shinji's first attempt to control Unit-01 ends almost immediately in disaster. The Eva stumbles, and the Angel closes in before he can recover. Its attacks damage the machine while Shinji freezes inside the cockpit. He next awakens in a hospital room without a clear memory of the battle's outcome. Gendo remains distant, and Nerv initially arranges for Shinji to live alone. Misato objects to leaving him isolated and takes him into her apartment instead. On their way there, she shows him Tokyo-3's buildings rising from underground and tells him that this is the city his actions have helped protect.
The apartment offers Shinji a confusing welcome: Misato's easygoing habits, discarded food containers and beer cans hardly match her commanding manner at work. Their household also includes Pen Pen, a penguin whose sudden appearance startles him. Alone in his new room that night, Shinji remembers what happened after he lost control. Unit-01 reactivated on its own, regenerated its damaged arm and tore through the Angel's protective field. The creature destroyed itself in an explosion, but the Eva survived. Shinji then saw the living eye beneath its damaged helmet and screamed. Misato praises him from outside his bedroom, while he curls up with the memory.