This is a rather dark one. Throughout the fic, there were a few moments where people would mention that Charlie looked like a guy. At first it seems to be simply a running gag at her expense and that's it. But after Eddie shoots her in the head, all of those moments make more sense. If the fic never mentioned how androgynous she looked, Eddie mistaking her for a guy would've been less easy to accept.
So Charlie has hints of being abusive in various ways; mostly physical, but also emotional as well. Nate's father was physically abusive and his mother was implied to be emotionally abusive. Charlie and Nate were romantically involved at one point, and in the revamp they're still sleeping together. The implications of this are rather unnerving.
There have been parallels made in the revamp between Vaughan and Casey. Vaughan and Nate are sleeping with each other in the revamp, and in the original they turned out to be in love.
This can mean one of three things (all being subconscious); either Nate has an Oedipus complex, sleeping with people who remind him of his relatives is his way of coping with his childhood, or he's drawn by people like his family members due to emotional trauma.
Even if Jude hadn't be captured by the doctors he most likely would've ended up dying anyways. He's emotionally unstable but using weed to cope. However, his supply wouldn't last forever. There Are No Therapists, so Jude would've had to deal with all his emotional issues on his own. He was on suicide watch before, so what do you think would've happened?
As funny as Jude is, in reality he is a inconsistently coherent, drug dependent, emotionally fragile man.