Past Sins/Tear Jerker

"Nyx: You have nothing to say... fine, because your actions have said enough already. You conspired with Celestia, you let her take me away. You abandoned the only pony you called a daughter. I guess I know now just how little I meant to you.
 * From Chapter 6:
 * There is something sad about seeing Nyx breakdown when she realizes that she's Nightmare Moon reborn and how torn up she is because of her past actions. It's even worse when you consider that Twilight tells her she's not Nightmare Moon, only for Nyx to find out the hard way that Twilight was wrong.
 * From Chapter 10:
 * The scene where Celestia takes Nyx away from Twilight so that she can ascertain Nyx's true identity, especially when Nyx cries out "MOMMY!!!" for Twilight, snapping her out of her Heroic BSOD an instant too late.
 * Nyx (after being transformed into Nightmare Moon) to Twilight Sparkle:

I am ashamed that I had ever called you my mother."

"Twilight: Please... please... we can’t let her... please, I need help! I can’t... I can’t help her by myself. I’m not a doctor, I’m not even a nurse... I need help... she needs help! PLEASE!"
 * Chapter 13:
 * The mayor delivering the heartbreaking news of Nightmare Moon's triumph to the population of Ponyville.
 * Chapter 15:
 * Nyx talks to Twist, who's happy to see her because she's still Nyx, her friend. Then Nyx gives her the CMC cape the Crusaders gave to her earlier so Twist can be an honorary Crusader and play with her friends. And she's happy for once since turning into Nightmare Moon. Obviously doubles as a Crowning Moment of Heartwarming.
 * Nightmare!Nyx sending guards to the library to get her a book she hollowed out and filled with her treasures from her time as a filly... her original CMC cape, her ribbon, and her kazoo, among other things. Then she picks up the kazoo and blows on it. You just wanna hug her and tell her it'll all be all right.
 * From Chapter 16:
 * Nightmare Moon's talk with Twilight in the ancient castle. All of it.
 * Both the end of Chapter 17 and Chapter 18 fits this in their entireties.
 * Twilight screaming at the crowd to come help her is a tearjerker.

"Nyx: You promise you won’t let her banish me, but I’m still scared. If we’re going to release Celestia and Luna, and if you can’t stop them, I want one last memory. Just one last, good memory... something I can hold onto if the worst should happen.
 * Chapter 19
 * Twilight and Nyx talking after deciding to release the Royal Pony Sisters from banishment. (Doubles as Crowning Moment of Heartwarming)

Twilight: Equestria can wait a couple hours. You can have that good memory, even though I promise it won’t be your last. So... are you hungry? I could go get us something to eat from the castle kitchens.

Nyx: That... that does sound nice, and... after we eat... could we read a book together, like we used to?

Twilight (trying to keep her voice strong, through it had an audible quiver): Of course. What story would you want to read?

Nyx: You pick, Twilight... you always pick the best stories."