- "Funny Aneurysm" Moment: While trying to figure out the cause of Sunflower being completely untouched by magic, Twilight consults her magical biology professor Moonlight Glimmer. Since the show introduced Starlight Glimmer, a villain who can completely remove a pony's cutie mark magic, a number of commenters have drawn a connection between the two:MLai: BTW, Prof. Glimmer. Did you know that your daughter is now a radicalized extremist wanted for crimes against royalty?Hoopy McGee: I am so tempted to make that canon in the story...
- As of Harmony chapter 22, it is, insofar as Professor Glimmer has mentioned having a daughter who's pretty adept at magic.
- Harsher in Hindsight: Celestia's story to Twilight about Queen Sapphire the Vile, a unicorn tyrant who punished disloyal or disobedient ponies by separating them from the magic field, likewise brings Starlight Glimmer to mind.
- Hilarious in Hindsight: Fluttershy rejects watching Grave of the Fireflies because she can't bear the thought of what happens to the fireflies (not knowing anything about it beyond the title). The episode "Power Ponies" has her Hulking Out after the villain attacks a firefly in front of her.
- Jerkass Woobie: Malachite, for all the things he did during the story, he didn't deserve to have his mind raped and reduced to have the mind of an infant.
- Moral Event Horizon: Velchiek chemically altering Erin's mind to keep her from revealing the truth. The discovery of this immediately leads to his removal and arrest.
YMMV / Project Sunflower