- Shinji calling his father out twice. The first of them when his father planned goading him into piloting Unit-01 for -what Gendo believed- first time. And the second when Shinji walked into his office and communicated him what he was piloting ON HIS TERMS, and he also demanded a prize for risking his neck (all the while trying not showing he was still frightened of his father).
- Asuka and Shinji fighting Gaghiel in Unit-02. They are losing because Shinji can not focusing properly, when he thinks of reminding Kyoko her daughter is about to die. Instantly Unit-02 goes berserker and easily opens Gaghiel's jaws. Asuka and Unit-02 reached perfect synchronization right then.
- The race of the Three Children in Chapter 16.
- Meta Example: The fact that Chapter 17 EXISTS is a He's Back moment of a monumental scale. Remember, the last chapter had come out four years ago, and the last snippet of a chapter had come out two years prior. There was no prewarning, and many had thought it had gone the way of most fanfiction... then Chapter 17 came out.
- It doesn't hurt that the solution to Sandalphon was also a Moment of Awesome. Shinji had been having In-Universe Nightmare Fuel over how CLOSE Asuka came to dying against Sandalphon, attributing to a lot of his Knight in Sour Armor nature (that is, the part that wasn't fueled by the memories of her actual death). In fact, it was bad enough that he outright questioned the operation (not that he wasn't absolutely right. As a matter of fact, if Asuka hadn't been effectively insulted by SEELE, even SHE wouldn't have been willing to do the operation. Unfortunately, this causes Ritsuko to decide Shinji should not be brought along. A fatal mistake? It would have been... if Shinji's overall changes to Rei hadn't caused HER to do his role in saving Asuka.
Awesome / Once More with Feeling