When Crosspatch and Lazybug finally discover what became of their parents after the Zap-O-Lantern fiasco, they end up helping Twilight Sparkle uncover a significant gap in Equestria’s recent history.
Comic version: http://lister-of-smeg.deviantart.com/gallery/53179306/Crystal-Heart-Attack
I didn't actually read the story, I read the comic version instead. That said, this was a heck of a tale, with quite the twist indeed!
It goes to show that you NEVER make a mother angry