We also learn that They then turn into more Pandora Shells, but remain conscious, trapped in their own minds and bodies, unable to do anything till they are unleashed as spores once more.
In "Mind Games," Jaune finds his father's... Mental image or something... In the latter's mind. Jacques has been nailed to a chair with a hundred bone spikes through his arms, legs, and chest, and has Overdrawn at the Blood Bank.
Jaune's first encounter with Malkuth. Though he's fought plenty of tougher foes before, this is the first time he's been completely, utterly outclassed, and it shows.
The training of the seven Arc sisters and its effects on them. One wonders what would have happened to Jaune were it not for Gamer's Mind.
Bianca: A lot of painful things, we all started about the same age, six or seven years old, and she trained us until we were ready to go off to Signal. That's what she always called it, making sure we were ready. That's what she said when she hurt us. I... I was the oldest, so it happened to me first, but even when she broke my arms, it didn't hurt as much as watching it happen to the others. I was nine when she started on Violet and eleven when she got to Sienna and Shani. She was just starting on Azure when I was leaving for Signal and I remember how it felt to leave them behind, knowing what they'd go through without me. There was nothing I could do, I know that, but I felt like a coward, like I was abandoning them. I hate to do this to you, because I know how she was like with you, but she hurt us so bad, Jaune — and when you hurt one of us, you hurt all of us. For six years, I came how knowing that she was waiting for me, for all of us, and that there was nothing I could do to stop her.
In "Puzzles," Jaune reassembles a giant pyramid and discovers that it has bloodstains going all the way from an altar at the top down to ground level. Can you imagine just how many people must have been sacrificed on it?
As the story goes on, we learn some very disturbing things about Babel. Long story short, Mengele and Unit 731 would have approved.
The Archangels may have overthrown their creators but they were not always better. One sign of their growing detachment from normal mankind was that, when an experiment was interrupted by agitators, one of them, Gevurah, decided that the best way to deal with it fast... Was to kill them all. Well, he did deal with the situation in less than five minutes...
The fate of Cinder's stepmother and stepsisters. The stepmother was found as a charred corpse, while the stepsisters were never seen again... But parts of them were found in the stepmother's stomach. No one knows how that got in there, and it's probably for the best that what happened remains unknown.
Malkuth himself. He may not actually be a capital-G God, but he is so absurdly powerful that he can fake it very well. He seeks the complete extermination of mankind for the suffering that we have inadvertently caused him and has murdered millions if not billions through the Grimm. The only reason he hasn't finished the job is because he was waiting for Keter to reincarnate. Even working through an Avatar that only can access a fraction of his power, he is still far stronger than all but the most powerful Huntsmen.