City of Ashes
- Alec's reaction to Jace referring to Magnus as his boyfriend in Chapter Twelve hits home for anyone who struggled with coming out. Becomes even more painful when Magnus is clearly upset by Alec's choice to deny the fact that they're in a relationship, but goes along with it because he respects the fact that this has to be Alec's decision.
- Jace calls in a favor with Raphael Santiago and uses one of the vampires' flying motorcycles to visit Valentine on his ship. Not to try and fight him or steal information, but because he's drowning in guilt and desperately lonely.Valentine: Why are you really here, Jonathan?Jace: I had to talk to someone. The Lightwoods— I'm nothing but trouble for them. Luke must hate me by now. The Inquisitor wants me dead. I did something to hurt Alec and I'm not even sure what.Valentine: And your sister? What about Clarissa?Jace: She's not too pleased with me either.
- The reason why Inquisitor Herondale is so vindictive towards Valentine? She lost her son, daughter-in-law, unborn grandson (ostensibly), and husband within days of each other, because of Stephen’s membership in the Circle.
- Just when she finds the courage to tell him that she still loves him, Jace tells Clary that he has decided to try to become a proper brother to her. Ouch.
City of Glass
- Clary and Jace's messy fight in the Lightwood Manor in Alicante. Jace deliberately insults Clary with the harshest words he knows will hurt her, so she will be tempted to leave him and go back to New York. When this is all done, Jace vents his frustration by punching a window.
- Amatis' backstory. She married Stephen, the love of her life, only for Valentine to force Stephen to divorce her just because her brother turned into a werewolf. In her anger, she vented her frustration at Luke and told him to never contact her again. She came to regret this as she grew older, just in time for Luke to actually follow her wishes and stop talking with her.
- Clary and Jace finding the horribly abused and injured angel Ithuriel in the Wayland Manor. The moment he breaks free, Ithuriel kills himself to end who knows how many years of torment at Valentine's hands.
- Max's death. What's worse, Sebastian did not actually mean to kill him, just to shut him up so he wouldn't have been able to alert the others about what he is going to do. He was merely collateral damage.
- Jocelyn finally coming clean to Clary about her past. As a Circle member, she was sheltered from knowing about the organization's shady dealings, so she only got suspicious by the time she gave birth to her son, whose demonic qualities repulsed her. Then when the uprising happened, she tried to escape Valentine, only for him to burn down the Fairchild Manor, killing her parents, and then made her to believe that their son also died with them. That was the reason why every year she cries holding a box containing the bones of Jonathan, the son she never had the chance to love.
- Valentine killing Jace. All the while, Clary is silenced, so she can do nothing but stare in horror.
City of Fallen Angels
- Simon being banished from his house by his mother, who freaks out upon finding out that her son has turned into a vampire and slowly descends into a madwoman.
- Jace’s mental health in this book. He is barely eating, having nightmares and not sleeping because he is afraid of his dreams and can't bring himself to tell Clary or his family.
City of Lost Souls
- Amatis being turned into an Endarkened.
- Magnus breaking up with Alec upon finding out that he was searching for a way to make him mortal without his consent. Still, his last words betray what he feels at the moment:Magnus: Aku cinta kamu.
City of Heavenly Fire
- Jordan dying on Maia's arms after Sebastian stabbed him. Hits a ton of bricks when it's revealed that, right before they arrived at Praetor Lupus, she had planned to break up with him.
- Maureen reveals that she was tortured and turned into a vampire by Camille, simply because she knew that she was close to Simon. Up until her death, Maureen believed that Simon would come for her, when in fact he didn't even know she was being targeted because of him.
- Raphael sacrificing himself to save Magnus. Made especially painful by the the nature of their relationship in ‘’The Bane Chronicles.’’
- Despite everything she's done, Maureen's death is surprisingly somber. When she realizes that she is dying, she only cries out a word: "Mama".
- A twelve-year-old Julian Blackthorn is forced to kill his Endarkened father to protect his younger siblings, setting up the action for the next series.
- As the Endarkened drop dead after the Infernal Cup is destroyed, Amatis can only give Luke one last loving look.
- Sebastian's death. Jocelyn cradles him as he says his dying words, his black eyes turning green. This was Jonathan Christopher Morgenstern, the brother that Clary should have had.
- Simon sacrifices his immortality and memories in place of Magnus'. He lives the next six months blissfully unaware of the fact that his friends, and Clary in particular, are painfully watching him from the distance.
