Each of them has saved the world. And each other.
New Game Arc
- From the beginning, players were incredibly sensitive of Shinji's perspective and went to great lengths to ensure his contentment and adjustment to being a pilot. Apart from assigning him a counselor to work on his anxieties and frustration, Misato developed a hide-and-seek game with a miniature Unit-01 figurine to let him distract himself with something silly.
- Misato takes Shinji and Rei to a familiar cliff-side overlooking Tokyo-3 from canon to give them a Rousing Speech on the significance of their efforts. They then have a small picnic, with Rei being surprised and appreciative of Shinji making food for her as well.
Friends and Figurines Arc
- Misato prods Shinji into giving Rei a figurine of Unit-00 as a gift. Later, they visit her apartment to find that she has placed it beside Gendo's cracked pair of glasses and a yellow paper frog implied to also be from Shinji, who had been practicing origami. Fans of the series will recognize the importance of this gesture, as well as the significance that she has more items from Shinji than from Gendo.
- Shinji befriending Toji and Kensuke. The more things change, the more they stay the same.
- To encourage Shinji's interest in cooking, Misato buys him expensive kitchenware and and a rare book on English cuisine. Although her motives may have been slightly selfish in nature, his skills improve as well as his confidence.
The Red Demon Arc
- As part of her regular check-up on Shinji's feelings and mental state, Misato realizes his feelings towards her are more positive than she imagined.
"Shinji's grown to rely on you a lot, to the point where he's often willing to accept your opinion even when it conflicts with his own, sometimes without realizing he's doing so. He also has a fairly high amount of respect for you, even though he realizes you're fallible. You don't tease him as much as you did at the beginning, so he now finds it unusual. You think his feelings towards you actually approach familial love. All in all, Shinji really likes having you as a guardian."
- A comedy movie night raises the spirits of the children, to the point that Rei cracks a smile and eventually laughs. Misato's narration is at a loss to describe how surprising this is.
- Rei takes issue with Asuka's slapstick reaction to Shinji accidentally seeing up her skirt, resulting in a minor scuffle. In a short frame of time, she has grown very attached to the few people to have shown kindness to her and is willing to fight on their behalf.
Moving Pains Arc
- Misato decides that it would be best to move all the children under one roof, and chooses a homey inn with a hot spring, beautiful scenery, and some distance from NERV HQ. Shinji's response is simple, yet speaks volumes:
"Shinji's happy here."
- Misato admits to Shinji, Rei, and Asuka that she loves them as her own. Shinji is extremely happy and responds in kind. Asuka's response is more conflicted and tearful because of her Dark and Troubled Past but she accepts the gesture. Rei, too, appreciates Misato and later comes around to recognizing that she feels the same.
- After Asuka is badly injured and left with several scars from an Angel battle, Misato decides to take the girls on a shopping trip to expand their wardrobes. Upon return, it is revealed that this was a ploy to get Asuka out of the inn so that Shinji could cook up a German-themed dinner for everyone.
Sealed With A Kiss Arc
- Rei makes her feelings for Shinji known, and he reciprocates.
- After Asuka comes to the realization that she has feelings for Shinji as well, she becomes conflicted about what to do and is advised by Misato to see for herself how Shinji feels. Meeting in private, the Love Triangle discuss how they feel about one another: Shinji says that he doesn't share Asuka's feelings, especially after Rei had already confessed, and Asuka is crestfallen. However, Rei takes her hand and says that while she may feel romantic love for Shinji, she feels familial love for Asuka and wants both of them in her life. Asuka decides she can live with that.
Mutual Interest Arc
- Mari's interactions with Advice and Trust Kaworu in a non-canon omake. At first she's excited by the prospect of messing with a version of Kaworu who's not already used to her, but after it becomes apparent he's having a tough time, she does her best to comfort and support him.
The Future Soon Arc
- Although it is interrupted by the sudden arrival of Kerubiel, everyone shares a sweet scene of contentment in their home's hot spring together. Asuka teases Shinji about thermal expansion, Rei enjoys being beside her aforementioned boyfriend, and Mari and Kaworu play-fight one another while Misato looks on proudly. It sums up the family dynamic in a short, simple, and beautiful moment.
Final Hours Arc
- How is the world saved? Through the Power of Love. The love and trust of Misato and the other Children motivate Kaworu to defeat the will of Gendo Ikari and Adam and save all of humanity. This act not only prevents Third Impact, but permanently rids him of his Angelic drives that would push him to try to merge with Adam. The Angel of Free Will becomes truly free.
- The last scene of the story. Misato embraces her Children one last time before they part ways, having fulfilled her duties as their guardian and parent and now forced to let them stand on their own two feet.