Misato is given the one Crowning moment the series, and most fanfics, denied her in the seventeenth chapter against the Angel ADAM.
"My name is Misato Katsuragi," she says, "Lieutenant Colonel of NERV. Daughter of Shiro Katsuragi, the stupid son of a bitch who woke you up. I am the daughter of a murdered man and the only human being to look on you with their own eyes and live to tell about it. I am the right hand of retribution and the last human being you will ever see, you glow in the dark mother f___er. Now smile asshole. Because this, is my seventeen years of f___ing payback!"
Just as a note, she can back this up with a JSSDF Self-Propelled Positron Cannon. This is followed by Kaji saving her from what she thought was a suicide attack with a shield grenade.
Asuka gets the second half of chapter 24 and all of chapter 25 as a protracted CMOA. Having been thoroughly broken by parental neglect and emotional/mental abuse before the fic began, and spending much of the fic itself as a stammering, timidwreck - It Makes Sense in Context - her rampage of awesome begins in a deliciously just fashion when she chairshotsKyoko, the parent in question. And then she really gets started....
She tops this one in ch. 38 when her various personality splits come to life to help her fight the Angel Iruel.
Two right off bat in chapter one before even the title, both for Yui Ikari: The first because it makes the entire fic possible, Yui Ikari aborting the contact experiment with unit 01. With one small act a brand new world of Evangelion was born. The second is this an example of how whipped Yui had Gendo:
"Kozou and Gendo both nod, both sighing. The technicians hide their snickers. There is little illusion of who wears the pants in the Ikari household, and it is mainly because it is easy to stay on Doctor Yui Ikari's good side that harmony rules GEHRIN with an iron fist."
Shinji meets Rei as she hits Sachiel in the Core with a rocket launcher and the ensuing chase across the city.
Rei killing a leftover part of Sachiel with her bare hands and leaving completely covered in Angel blood.
In chapter 30 we learn what she did with the body, I think Rei explains it best:
"Well, then I had him stuffed. And mounted. And I installed hydraulics in his arms so he'd sort of jump anyone who looked in my closet. And stuff."
In Chapter 40 canon-Shinji opens the closet...
Chapter 38... Where the hell do we even start?!Iruel shows up and merges with the Cherubim, Asuka's split personalities kick butt and take names, Gendo snipes a TRIDENT to death, Jet Alone Prime gets a "soul" and becomes basically a mechanical Evangelion, topping it all off with Go-Kun and Rei dishing out the most epic Giga Drill Breakah this side of Gurren Lagann. Ya know what? Let's just call it a Crowning CHAPTER Of Awesome.
Chapter 40: Kyoko's confrontation/verbal beatdown of Unit 02/the canon version of herself after finding out her own and Asuka's canon fates. Also a CMOH.
Chapter 42: Rei dragging ADAM into the End of Evangelion setting so that she can administer a proper beatdown that involves the rearranging planetary geology, while also rescuing the Shinji and Asuka of that world. Oh, and the Eiffel Tower gets used like a Javelin.
Also one for Adam during the chapter, after Rei asks if that's the best he can do. Adam's response is:
"ADAM's eyes flash. From orbit on this dead world, one can see the entire Japanese Archipelago shatter."
"As the Pacific rushes in to fill the gap, Go-kun hops between still floating chunks of island, floating in the air from the power that warps gravity and space around it, with ADAM at the center of the maelstrom. The light surrounding Him becomes a cyclone of destruction and rage, ripping into the crust beneath before exposing the red hot mantle."
"A bellow of rage from the Giant of Light, and behind him Asia begins to crackle and fold backwards, unraveling like badly stretched plastic wrap. The Pacific boils, clouds of red filling the air..."
Also in Chapter 42, taking the focus of Rei for a moment. Gendo, the Crazy AwesomeManipulative Bastard we all know and love gets one when he confronts Canon!Yui leading to the conversation ending with... well, for those who want to see, it's on the Quotes page
Pieter Sohryu taking out a mini-Angel with a V-22's cargo bay door.
Rei chapter 45: Getting ADAM and Cthulhu to fight each other.
Then Rei bumping fists with Nyarlathotep and getting his autograph for her sister.
Rei nods, holding up her fist. The Black Pharaoh bumps his fist against hers, the collective sanity of the cosmos shuddering for a moment and inexplicably causing the Migou race to collectively question their physical waste management abilities.
"Look me up in a few thousand years," the Bloody Tongue says.
"Deal," Rei says, holding out a notepad, "For my sisters."
The emissary of the Outer Gods produces his pen, signs the paper, and watches her skip off into the portal, which disappears after her.
While there are many from the crossover arc (too many for one troper to go through in one go) this one has to go on here as both a crowning moment for the fic and especially for the Author.
Earth: Designation CANON.
At the heart of Instrumentality, he finally realizes the lesson he was taught those months ago, when the visitors from the other world ended up on his world. He finally realizes how he's been betrayed.
Who was the greater monster, he asked.
Now he knows. Now he knows by far.
And in the heart of Instrumentality, at the center of the collective Godhead that was the human race, he makes the decision he could have made so long ago, but finally makes now. And striding forward, past the despondent Shinji, still half blinded by the pain of his missing right hand, he wraps the gloved left hand around Yui Ikari's throat as she stares at him in disbelieving shock.
"God damn you," Gendo Ikari roars, "Get away from my son!"
And a new day dawns on Tokyo-3.
And thus in a brilliant move Gregg Landsman has "Nobody Dies" cause one of his earlier fanfics, "Walking in the Shadow of Dreams".
Asuka has all of chapter 18 too, working round the clock for five days to get Shinji out of the Dirac Sea as she continually talks to him about how he's made her realize her own worth for the first time.
After chapters upon chapters of waiting and biding his time, Zeruel has, at long last, had his patience tried for the final time, and after venomously slamming Kaworu for his failures in his eyes, he finally decides that enough is enough, and descends to Earth. And it is glorious. The expected reactions from the cast will likely be the same.
For his first trick, Zeruel curb-stomps three Cherubim.
But not before cleaving Mt. Everest in half.
Combined seamlessly with Crowning Moment of Funny, Gendo's epic fistfight with US President Stephen Colbert, followed by his convincing an immeasurably pissed off Yui that he'd planned the whole thing, and getting her into the sack.
Shinji takes advantage of the bizarre laws of physics in a pocket universe to kick Adam's ass with his bare hands.
Kouzou in Chapter 60, taking down a group of terrorists Rei style.
Pieter's What the Hell, Hero? to Yui when she disapproves of Shinji and Asuka having sex, pointing out there were all kinds of ways she could have stopped it, all while spilling his guts about what a lousy father he's been and contributed to Asuka's crappy life that led to this moment.
Misato becoming Go-Kun's pilot to take down Raziel, with assistance from Asuka.
Greg Landsman has his own with Chapter 66. After the last chapter ended with some unspecified problem with Shinji that left both his parents horrified, we spend this chapter watching him stuck in Unit 01's core, and things carry on perfectly normally from there with the reader fully able to buy this is what they were talking about...until a Rocks Fall, Everyone Dies ending, after which we learn it was All Just a Dream. And the truth about what happened to Shinji is even worse. A real storytelling tour de force, with the HSQ off the scale.
Two big ones in Chapter 69: Uriel getting Zwei to accept him as a pilot, enabling him to fight Zeruel including scraping his face against the wall for the entire ride up a launching tube, and the He's Back moment for Unit 00, powered by Mari.
Quite a few in Chapter 70:
Kyoko scolding Ichi out of her Heroic BSOD and getting her to open up so they can save Zyuu.
Shinji fully tapping into his Nephilim powers and making physics his bitch while fighting three Zerulim.
Asuka killing two Zerulim, revealing the firepower she's built into her plugsuit.
Chapter 18. Shinji, through sheer force of will and determination, fights back the stamina-draining effects of the Dirac Sea, literally crawls his way to Unit 01 so he can escape. And what's his response when an enraged ADAM grabs his leg in an attempt to stop him? Kicking him repeatedly in the face to shake him off.
Chapter 86: Ichi fully snaps out of her Heroic BSOD and evolves into an adolescent personality, also gaining the ability to teleport, which she uses to completely Curb Stomp Tamiel. And when The Beast causes her to shut down, Shinji is right there prepared to fight it off.
Rei, but only after a bit of a fridge moment. Consider this: Rei, from this universe, is known as Terrifying!Rei. Okay, keep that in mind for a moment. Now, at one point, she visits the world of Aeon Natum Engel, where she meets her counterpart there. This is known, to fandom, as Creepy!Rei. Think on this for a moment. ANE Rei is a precognitive EldritchAbomination who lives in a world where the local NERV-equivalent fights Eldritch Horrors rather than Angels, and this includes CTHULU. And yet, ND Rei is known as Terrifying. That's right, the Rei from the world where the Necronomicon is coming to life and is used as science is less terrifying than the Rei from the ND universe.
Chapter 87: Both of Ichi's personalities put their heads together to come up with a plan to stop the end of the world: siphon the excess energy from the Lilith/Ramiel combination across all the Evas, giving them all new abilities which they quickly use to Curb Stomp Tamiel.
Shinji rescuing Mari from her own version of NGE's final episode, by punching Claire.
Ichi's first day of school, kicking Israfim ass with her backpack.
She easily trumps it by taking out a Cherubium. In her avatar body. While on fire.
Kyoko piloting Unit-07.
Lots of bee-like cherubim infiltrate NERV, seemingly unstoppable in their converting it to a hive...and then they meet Na00ko.