Contains spoilers for this episode and earlier episodes.
Nerv retrieves Unit-01 after the Angel's beam badly damages it, and Shinji is rushed into treatment. The enemy then begins drilling through the defenses above headquarters. Tests establish that approaching it directly invites another devastating shot, so Misato proposes a distant attack with a positron rifle. Breaking through its protective field will require electrical power gathered from across Japan. Nerv requisitions the weapon and prepares a shield for Unit-00, assigning Rei to protect Shinji while he fires. Still shaken by his injuries, Shinji hesitates to return. Rei offers to take over, but he eventually joins the operation rather than leaving everything to her.
Before the attack, Shinji asks Rei why she pilots. She speaks of the connections she has through the Eva, while her farewell sounds to him as though she does not expect to return. Their first shot coincides with the Angel's own beam, and the two attacks deflect each other. While Shinji prepares another round, Rei steps in front of Unit-01. Her shield absorbs the next beam until the heat overwhelms it and damages Unit-00. Shinji fires again and destroys the Angel. He then forces open Rei's entry plug, finding her alive. His relief brings tears, and when she cannot decide how to respond, he suggests a smile.