The story begins in a club in New York called Pandemonium. Clary and her friend Simon decide to spend a night out when Clary notices an unusual group of people. She follows them and she soon finds herself seeing a boy being murdered by three strange teenagers. She soon finds that the boy was a demon, and the other three people, Jace, Alec and Isabelle are Shadowhunters. Clary finds that other people can’t see Shadowhunters when Simon comes to her with a bouncer. Clary refuses to tell Simon what happened even if he realizes that something is wrong.
The next day, Clary gets in a fight with her mother and uncle, Jocelyn and Luke when she finds that she will have to spend the rest of the summer at a farm. She leaves with Simon and together they go to a café where Clary meets Jace once again. She follows him outside where she had a brief talk with him before receiving a strange call from her mother telling her not to come home. The line goes dead and Clary runs home only to find the door open, the apartment destroyed and her mother nowhere to be found.
She discovers that a strange creature is in the apartment and she has to fight with it as the creature tries to kill her. Clary manages to kill the demon with a Sensor, a device she took by mistake from Jace, but she is struck in the back of the head and loses conscious. When she wakes up she is outside and Jace tells her that he has to take her to The Institute because she got injured by the demon and would die otherwise.
Clary wakes up 3 days later in the Institute. She calls Luke but he doesn’t want to see her and even tells her to stay away from him. Jace thinks that Clary may be a Shadowhunter and that was why she could see them. Clary tells Hodge that the demon talked about a man named Valentine, a man who was supposed to be dead. Hodge decides that they best course of action is to inform the Silent Brothers and The Clave about the situation.
Clary asks for permission to go home to take some of her things and Hodge lets her but only if Jace goes with her. Once they arrive at Clary’s apartment, they notice claw marks on the door and a forsaken into the apartment. Jace kills it and before they leave they are stopped by Madame Dorothea who knows about the Shadow World.
Clary finds the building is actually a sanctuary and that Madame Dorothea has in her apartment a portal. She opens the door and is transported to Luke’s house, along with Jace who went through the portal as well.
They decide to inspect Luke’s house and they discover Simon who was looking for Clary. The three of them inspect the house but Luke appears with two men asking where the Moral Cup was and if Jocelyn had another child. After the three men go, Jace tells them the two men with Luke were the ones that killed his father when he was 10 years old.
Jace, Simon and Clary return to The Institute where Hodge tells Clary about The Circle, a group of Shadowhunters that wanted to stop The Accords from being signed. Their plot was stopped however and it was believed that Valentine, his wife and their child died in a fire. Hodge tells Clary that her mother was also a member of the Circle as she was Valentine’s wife.
Jace’s father, Hodge and Isabelle and Alec’s parents were also members of the Circle and they wanted to use the Mortal Cup to create a new generation of Shadowhunters and to kill all Downworlders. Hodge and the Lightwoods were punished by being sent to the Institute in New York.
One of the Silent Brothers, Jeremiah, comes and sees Clary but is unable to access her memories because someone put a powerful spell on her. He tells her that is she wants to find the truth about her memories she has to come to the City of Bones and be seen by the other Silent Brothers.
Clary agrees and Jace accompanies her to the City of Bones but even the Silent Brothers are unable to break the spell. A name surfaced however, Magnus Bane, and Clary believes that a link must exist between her memories block and that person.
Alec, Isabelle, Simon, Clary and Jace meet at a restaurant and Isabelle realizes that she has seen the name Magnus Bane on an invitation to a party. They end up going to the party and Magnus admits to putting a spell on Clary at her mother’s request that would make her forget all the creatures from the Shadow World as soon as she saw them. He is however unable to break the spell because Clary’s mind would be damaged in the process. He tells them that it is possible that the spell will fade over time.
Simon is turned into a rat after he drinks and unknown potion but Magnus refuses to turn him back to his human form because humans don’t handle magic as easy as Shadowhunters do. Clary puts Simon into her backpack but he is stolen away by a vampire.
Clary and Jace goes to the vampire’s lair and are helped to get in by a boy who later is discovered to be a vampire. The vampires attack Clary and Jace but they manage to escape with Simon after werewolves appear. They escape with a motorcycle used by vampires and Simon turns back to his human form.
When they arrive at the institute, Hodge gets mad at them for putting their life in danger. Later that night, Jace takes Clary to the greenhouse and kisses her. When he takes her back to her room, they meet Simon coming out of it and Jace gets mad at Clary. Simon goes home and Clary is left alone.
She realizes that by using runes she can take objects out of drawings and tells Jace what she has found out. She tells Jace and Hodge that she believes her mother hid the Cup into a drawing and gave it to Madame Dorothea as a tarot card.
Alec, Jace, Isabelle, Clary and Simon go to Madame Dorothea to take the cup. After Clary takes the Cup from the card, the portal that was in her apartment opens and a demon comes out of it killing Madame Dorothea and injuring Alec. Simon kills the demon and they take Alec back to the Institute to receive medical treatment.
Isabelle goes with Alec and Simon into another room while Clary and Jace remain with Hodge. He proves himself to be a traitor when Valentine appears and takes the Mortal Cup and Jace with him.
Hodge runs as soon as the curse is lifted off him and Clary runs after him. Hodge attack Clary but she is saved by a werewolf and she passes out. When she wakes up she realizes that the werewolf is actually Luke. He tells her that he used to be in the Circle and that he was Valentine’s parabatai. They figure out where Valentine must be hiding and together with Luke’s pack they go to get Jocelyn and Jace back.
They find Jocelyn unconscious and Jace who tells Clary that he found his father and that he is Valentine. Jace finds out from Valentine that Clary is his sister and that he killed his in laws because they betrayed him. Luke comes and starts to fight with Valentine but is injured. Valentine tells Jace to go with him to Idris but refuses and stays with Clary. They recover Jocelyn and they take her to the hospital while Clary returns to the Institute.