Contains spoilers for this episode and earlier episodes.
Misato repeatedly listens to Kaji's final message while Asuka withdraws to Hikari's home, unable to recover her confidence. Gendo faces Seele's anger over the loss of the Spear of Longinus, but another Angel interrupts their questioning. Rei launches in Unit-00, with Asuka intended to support her. Asuka's synchronization is now too poor for her to move the Eva, and she is withdrawn. The approaching Angel changes shape and penetrates Unit-00, beginning to merge with both machine and pilot. Rei experiences contact with a presence that takes her appearance, exposing a loneliness she recognizes in herself. Shinji is sent out when the threat extends toward him.
Rei decides to contain the Angel inside Unit-00 and destroys the Eva before it can take Shinji with her. The explosion devastates the city, leaving him grieving. Nerv later reports that Rei has survived, but the girl he visits does not remember saving him and refers to herself as a third incarnation. Ritsuko, sent to Seele for questioning in Rei's place, returns angry at Gendo's treatment of her. She brings Shinji and Misato down through the abandoned facilities beneath headquarters, showing them Rei's origins and the remains of failed Evas. Finally, she reveals the spare Rei bodies connected to the dummy system. Ritsuko destroys them and breaks down over having lost Gendo's affection.