When Emerald is rescuing Endymion from Beryl, he notices that Endymion's bed is rather large for one person and makes jabs at Endymion for "sleeping [his] way to the top". Thing is, at that time, Endymion was brainwashed by Beryl. If the two were really sleeping together, as Emerald mocks, then it would mean Endymion was being raped.
Pluto's involvement at the very end of the fic. Whatever her motives may have been, it's still chilling to imagine that someone is willing to erase an entire future and everyone in it, simply because it wasn't what she wanted it to be.
While his intentions were noble, Emerald still bathes the planet and everyone on it in a strange energy in the hopes that it will repel Purification. Every time Emerald has interacted with the Silver Crystal's power, it had violent, painful effects. Emerald even compares the interaction of his power and Serenity's to that of matter and anti-matter. While it turns out alright, he very well could have set things up for an Earth-Shattering Kaboom.
