When Miang is killed and Body Surfs to Elly, she takes Billy's gun and shoots Fei and explains a large amount of information concerning Deus. The only thing Billy can manage to say: "...She took my gun."
At Billy's orphanage, a sidequest involves collecing a bunch of comic books. A kid comes out of the bathroom and hands you one, saying that there wasn't any toilet paper and he used the comic instead. The item's description? Not so comical anymore
The whole "Bart Missile" incident. All of it.
And much later, Fei's reaction when he learns about it.
Fei: Bart... don't tell me...
Citan: It's true Fei.
Bart: (defensively) H-how was I supposed to know you were on that thing?