Family
Throughout the novel Clary struggles with the knowledge that Valentine is her father, as he commits unspeakable atrocities and seeks to use his children only for his own gain. She also struggles with the knowledge that her mother lied to her for most of her life, refusing to tell her that she was a Shadowhunter, and because her mother is in a coma for the entire book, Clary is unable to confront her. Jace also struggles with his family, as he believed for years that his father was dead, and now knows that Valentine is in fact his father. He is unsure of whether he belongs with the Lightwoods, his adoptive family, or his biological family.
Identity
Clary seeks to understand her place in the world as a Shadowhunter. As she was raised mortal, she’s never learned how to fight, and understands very little about the Shadowhunter culture. She doesn’t feel like she fits in with the other Shadowhunters, but no longer feels like a mortal either. Jace also struggles to discover his identity, because he has learned unspeakable things about his true family.
Prejudice
Many characters are the victim of prejudice, because the Shadow world is very conservative and unwelcoming of those who go against the social norm. Alec is reluctant to tell his parents that he’s gay, because he’s afraid of their reaction. The Downworlders face prejudice as well, because they’re considered second-class citizens to the Shadowhunters, so when werewolves and vampires start to go missing, the Clave pays very little attention to the problem.
Duty vs. personal feelings
The Clave is very corrupt, and as a result many of the orders they give to the Shadowhunters are controversial. Alec in particular has difficulty following orders at times, especially as the only member of the main crew who’s an adult. He knows that he has an obligation to do as the Clave orders, but often the commands he receives compromise the well-being of his friends and family. As a result he’s forced to make the difficulty decision of obedience or friendship frequently.
Good vs. Evil
Jace is perpetually unsure of himself. Upon discovering that Valentine is his father, he immediately begins to question whether he is good or evil- if his work with the Shadowhunters makes him one of the good guys, or if his parentage makes him a monster. The struggle is one he continues to face throughout the novel.
