The main characters, Clary Fray and Simon Lewis, are at a club where Clary witnesses a murder by a group of teens, and is shocked that Simon and the club's security guard, cannot see the killer—a boy called Jace, who claims that the boy he murdered was a demon. The next day, Jace offers to take Clary to meet his tutor, but before she can do so, she receives a distressing phone call from her mother. She returns home to find her mother missing, the apartment trashed, and a monstrous creature, a Ravener demon, lying in wait for her. She defeats the creature, but is injured in the process, and Jace takes her to his home. His home is called "The Institute", an old gothic cathedral in New York that humans, or mundanes, can't see, because it is concealed magically by glamour. Here, she recuperates. She also meets Hodge Starkweather, Jace's tutor, as well as his adoptive-siblings Isabelle and Alec Lightwood.
Returning to her apartment with Jace, Clary is attacked again by a monster called a "Forsaken", which Jace kills. They escape through a magical portal in to Luke's, a family friend's, house, where they meet Simon and overhear a conversation between Luke and two men who Jace reveals to have killed his father. They return, with Simon, to the Institute and recount the conversation to Hodge, who in return tells them the tale of a group of '"Shadowhunters", or demon hunters who are invisible to humans, known as "the Circle", who attempted to kill all "Downworlders", or vampires, fairies, warlocks, and werewolves. Although the Circle's leader, Valentine, was supposedly burned to death, Hodge feels that Valentine may have survived. Hodge also reveals that he, the Lightwoods, Luke, and Clary's mother were all members of the Circle.
Hodge then acquires the help of a monk with magical powers, called a "Silent Brother", Jeremiah, to discover how Clary is able to see Shadowhunters and why she was attacked. Jeremiah discovers a block on Clary's mind, and takes her and Jace to the City of Bones, where the Silent Brothers attempt to break it. Although the attempt fails, Clary discovers flashes of information, particularly the name Magnus Bane, which, with Isabelle's help, Clary traces Magnus Bane to a party, which she attends with Jace, Simon, Alec and Isabelle. There, they discover that Magnus is the High Warlock of Brooklyn, and he placed the block on Clary, although his attempts to help her remember are unhelpful. During the party, Simon is turned into a rat by a faerie drink, and Jace and Clary have to rescue him after he is taken home by a vampire...
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El libro comienza cuando la protagonista, Clary Fray, observa a un extraño chico con el pelo azulado que estaba en la entrada del Club Pandemonium. Más tarde, dos chicos sospechosos van tras el chico de pelo azul, por lo que Clary decide avisar a su amigo Simon, pero él no ve a nadie y, creyendo a Clary, va a buscar a un guardia. Justo cuando uno de los chicos está a punto de matar al chico de pelo azul, Clary se involucra ante sorpresa de todos. El chico de pelo azul, que es un demonio, trata de escapar, pero es asesinado por uno de los muchachos e inmediatamente desaparece su cadáver. Clary descubre entonces que los chicos no son asesinos, sino cazadores de sombras, una antigua raza creada mediante una mezcla de sangre entre el ángel Raziel y un humano, los cuales con frecuencia usan runas para ser invisibles a ojo humano y asi ser protectores de la humanidad.
La siguiente noche, cuando Clary y Simon van a un bar(Java Jones) para ver el espectáculo de un amigo de estos, se encuentra a Jace, uno de los chicos de la noche anterior. En ese momento, Clary recibe una extraña llamada de su madre e, inmediatamente, se dirige a su apartamento, donde es atacada por un demonio rapiñador. Jace la encuentra herida y la lleva al Instituto, el lugar donde él vive y entrena para matar a los demonios.
Allí Clary conoce a Hodge, el tutor del Instituto, que le explica que su madre fue una cazadora de sombras. También le dice que su padre fue el que envió el demonio, con el fin de obtener la Copa Mortal. La Copa Mortal, es el único objeto capaz de crear cazadores de sombras utilizando humanos.
Clary se da cuenta de que ella es la única con la capacidad para recuperarla, y lo tiene que hacer a tiempo para salvar a su madre y decidir el destino del mundo.