In particular, Chapter 21. The chapter itself is nothing but From Bad to Worse for Asuka. Then the ending rolls by, and as the author put it (After someone described an alternate, intensely depressing way to end the chapter):
This is certainly now a nightmare scenario for everyone involved. And it would have happened and would have been the way the chapter concluded- if Shinji didn't go into her room at the end of the chapter and settle things with her. The problem is, Asuka has three pillars her life is built around, and Kyoko managed to kick out two of them in just two minutes. And now Shinji's built one of those pillars so high she can see her apartment from the top of it.
"I can fix this."
Just before their first kiss, Asuka was slipped a roofie and Gendo and Shinji had to step in to save her. Asuka, naturally,begins apologizing for it, until Shinji insists to her that he doesn't "put up" with her and she's worth it all, proceeding to list all the reasons why until Asuka... shuts him up.
Chapter 13, when Shinji threatens a pilot's strike if Asuka isn't released from the hospital. Which would've meant no active Evas. For Asuka's sake, Shinji effectively put a gun to the head of the world.
In her own strange way, Kiko, one of the Ree, gets one in chapter 28, when she hacks the MAGI, breaks out of NERV, and steals a plugsuit just so she could spend time with her brother.
Ch. 36. Misato and Asuka. Kaji and Shinji. 'Nuff said.
In Chapter 38, Asuka's multiple personalities come to her rescue against Iruel's attempted Mind Rape, with Dollie giving a very heartwarming speech to Asuka herself.
Chapter 40. ND!Gendo is struggling with the idea that Yui might be dead and is contemplating suicide, but tells himself that everybody else is counting on him, and if Yui really is lost beyond recovery, then Canon!Shinji, who has been transported to the ND!Universe, will need a father.
Ch. 42, when Mana and canon!Shinji have a bonding/therapy moment that ends with them kissing.
Later on, while talking with canon!Yui through a spare Ichi avatar, Gendo threatens her with keeping canon!Shinji in the ND! universe when canon!Unit 01 gets sent back through the Dirac sea. This doubles as a CMoA for Gendo.
Ch. 44, when canon!Shinji convinces ND!Gendo to let him go back to his universe.
Chapter 45, in particular Yui's day with Ichi.
Believe it or not, Kyoko finally breaks down and takes a huge step toward reconciliation with Asuka.
Crossed with a Crowning Moment of Awesome, the end of Chapter 46 is one for canon!Gendo. "God damn you," Gendo Ikari roars, "get away from my son!"
Chapter 48 has Kei's reunion with Little Mommy. Happily, it didn't Go As Planned.
Ch. 54. Yui's talk with Kei after the disastrous evening.
In Chapter 55, Kei bonding with her sisters. Over Angel slaying, of course.
Also from Chapter 55, this scene:
"Yeah," Shinji says, "I could see this being Hatchi's idea, but Nana would put together the weapons. But Kei really thought out the design. Normally, the girls wreck Kei's stuff, but they really did miss her." "How d-do you know all this?" Asuka asks. He shrugs. "I'm trying to be a better brother."
Ch. 61 has Shinji and Asuka finally consummating their relationship, in no small part due to Lilith's Anti-AT Field. It was LONG overdue.
Shinji's encounter with the apparent Stalker with a Crush cosplaying as Asuka in ch. 63. Turns out she just wanted to thank him for saving her boyfriend from Gaghiel.
Kaworu admitting his feelings for Kei. That fact that he's so stupidly naive to the whole thing makes it even cuter.
It's quickly ruined by Makinami, but Kyoko trying to make up for her vicious insults towards Asuka while chaperoning the school dance by recreating the night for her and Shinji is a very sweet gesture.
Gendo meets Ichi for the first time, and tells her that he may come with Yui during her next visit.
Yui to Kei: "You were Naoko's project. You were Naoko's experiment. You are my daughter. Nothing ever changes that." Followed by Kei calling her "Mom."
Chapter 18. "This is Unit 01. I'm sorry if anyone was worried, but we sorta got stuck there for awhile." Cue joyous cheers from NERV personal.
From the same chapter, after the aforementioned event, Yui gives Asuka, who was instrumental in getting Shinji back home, two simple words.
Chapter 72, for all its hilarious awesomeness, also has a moving scene of Kyoko explaining just why she got so upset over Pieter saying Shinji and Asuka were just like them, and Pieter apologizing and assuring her that she isn't her mother, no matter how long it took her to realize her mistakes.
And the next chapter reveals that Rei set up the whole ordeal for Asuka to stream it onto the Internet and get her known as willing and able to beat up any girl who tries to steal Shinji from her, as thanks for Asuka being her first real friend.
Chapter 80: Kei gives little Mommy a hug.
Pieter laying into Claire for her treatment of Mari, also a Crowning Moment of Awesome: "Claire, it's one thing to suspect, but you went too damn far. It doesn't matter what the Hell Mari is! Because she's still my daughter!...I was there! I was there when I thought she died. She could have come back as a big floating...thing...and it wouldn't have mattered because I got my little girl back."
After the funny explanation that Shinji and Uri will be forced to room together until they can be civil with each other, at Asuka's request, Shinji points out how hard it's going to be, but that Asuka is worth it.
All of Asuka and Pieter's scenes in Chapter 84, as they truly start to bond for the first time.
Shinji and Uri finally apologizing to each other and putting their differences behind them.
Uri: And if you ever hurt her, I will break you like plate glass.
Shinji: If I ever hurt her, I will let you.
Shinji and Gendo interface with Ichi, and finally assure her that it doesn't matter that she's not really the unborn Rei, and they still consider her family. A Crowning Moment of Awesome follows.
What really cinches this is how Gendo Ikari, who had spent years bitterly hating Ichi for nearly killing Yui, fondly states "That's my girl!" as Ichi powers up. It truly shows how far he's come, and how different he is from Canon!Gendo.
Rei, after spending a whole chapter trying to form a sibling rivalry with one of the other Ree, decides to instead pour that boundless energy into being a good mother to the Reego.
Annette letting Omega look after her horses.
Rei in couples therapy with Go-Kun, learning that in some ways she is in a normal situation.
Shinji and Ichi's talk about her missing years.
This exchange between Shinji and Unit 01 in Chapter 17.
Unit 01: i am scared.
Shinji: I'm here. Don't be. He won't harm you while I'm alive, got it? If he wants to get to you, he gets through me!