This is pretty much a flashback episode of the actions being taken after second impact. Professor Fuyutsuki unraveled pictures of what really happened, and demanded answers from Gendou. He tells him the true intentions of the organization SEELE, and wants the Professor to cooperate with him in backstabbing them from reaching their one inhumane and immoral goal. In this episode, we discover the cause of death of Ritsuko's mother. Gendou and her had a secret relationship going on, and when the first clone of Rei appeared in front of her, echoing hurtful words that came straight out of Gendou's mouth, she killed the little girl and commited suicide shortly after. We also understand what had happened regarding Shinji's mother's disappearence. Apparently, she was fused with the EVA Shinji now pilots. The episode ends with Kaji being shot, and Misato crying over his death, while Shinji simply ignores her and continues to listen to his Beethoven soundtrack.
A lot of things were revealed in this episode and it hints us that Neon Genesis won't have the happiest of endings when you're not sure which side is truly good. While a lot of questions were answered, what was truly the main treat of this was how Shinji reacted to Misato. Obviously if Ash Ketchum was in his situation, he'd calm her down, but Shinji simply ignored the one person who loves him the most. For me, I was rather confused even if the concept itself is rather simple.moreless
