Contains spoilers for this episode and earlier episodes.
A flashback reveals how Rei was injured before Shinji arrived at Nerv. Unit-00 went out of control during an activation test and ejected her entry plug. Gendo rushed to open the overheated hatch with his bare hands, burning himself as he reached her. Shinji later learns the reason for those burns while Nerv examines the remains of the Angel he defeated. The story surprises him because it exposes a concern his father has never shown him. Watching Rei smile while talking to Gendo deepens his curiosity. Ritsuko gives him an excuse to approach his fellow pilot by asking him to deliver her replacement identification card.
Shinji finds Rei living alone in a neglected apartment, where she keeps Gendo's damaged glasses. His visit becomes painfully awkward when she emerges from washing and he accidentally falls against her. Rei shows more concern for the glasses than for his embarrassed apologies. On their way to Nerv, Shinji asks whether she is frightened of another activation test. Her faith in Gendo prompts him to criticize his father, and she slaps him. Unit-00's new test succeeds, but an approaching Angel interrupts the work. Shinji launches in Unit-01 to intercept it. Before he can mount an attack, a powerful beam strikes the Eva, placing him in immediate danger.