Contains spoilers for this episode and earlier episodes.
Unit-03 arrives in Japan for an activation test at Matsushiro, where Misato and Ritsuko supervise the preparations. Toji has agreed to pilot in exchange for better medical care for his sister, but Shinji has still not been told his friend's identity. Misato postpones the conversation again, while Asuka also avoids giving him the answer. At school, Hikari worries about Toji's subdued behavior and confides her feelings to Asuka. The new Eva's test ends in an explosion when an Angel takes possession of the machine. With communications to the site lost, Gendo assumes command and orders the three other Evas to stop the infected unit.
Asuka is disabled before she can tell Shinji who is inside the enemy Eva. Rei hesitates to fire and is attacked as well, leaving Unit-01 to confront it alone. Shinji sees that an entry plug is trapped in the machine and refuses to risk killing the human pilot. Even when the infected Eva begins strangling Unit-01, he will not strike. Gendo disconnects his son's control and activates the dummy system. Shinji can only watch as his Eva breaks the opponent apart and crushes its entry plug despite his pleas to stop. Misato survives the test-site disaster, but her attempted explanation comes too late: Shinji sees the wounded Toji being recovered.