Red letting Yellow raise a Rattata, and offering Gancena a Pokemon.
Gancena meeting a forest full of Pikachu, including Red's Pikachu's family, and catching one and naming it Ash. Even better is that the Pikachu wanted to go with her.
Hilarious in Hindsight: Giovanni's goal was vague in the games and was commonly theorized as wanting to capture Mewtwo, which he doesn't succeed at. In Pokémon Ultra Sun and Ultra Moon, where he did succeed in his plans, his team consists of mostly ground-types, but his final Pokemon is a Level 70 Mega Mewtwo.
Nightmare Fuel: The Thoughtless, especially since by their nature they aren't aware of what they're doing. It's compounded in-universe when Gancena sees an offshoot looking like Giygas, the Eldritch Abomination from EarthBound.