Contains spoilers for this episode and earlier episodes.
Misato faces questions about whether the previous Angel was trying to communicate with Shinji through Unit-01. His latest test results have declined, but Nerv soon has another crisis: its Nevada branch disappears during work involving Unit-04 and an S² engine. The surviving American unit, Unit-03, is to be transferred to Japan rather than risk another installation. Ritsuko discusses using the dummy system, which could operate an Eva without its normal pilot, but a human candidate is available for the arriving machine. Misato learns the chosen child's identity and hesitates to tell Shinji, fearing how he will respond after his recent ordeal inside the Angel.
At school, Toji is drawn into the new assignment while ordinary friendships continue around him. He accompanies Shinji to Rei's apartment, where Shinji cleans the neglected room and receives a surprised expression of thanks. Hikari takes an interest in Toji and offers to bring him a homemade lunch. Elsewhere, Kaji tells Misato that Marduk is a front and directs her attention to the pilots' school. He also shows Shinji his garden, speaking about caring for living things and the kindness that suffering can teach. Toji returns from a meeting with the principal looking subdued. Asuka discovers who the new pilot is, while Shinji remains outside the circle of people who know.