The book begins by presenting Valentine in a building in Manhattan with a young warlock named Elias. Valentine convinces the warlock to summon a very powerful demon but Elias is killed when the pentagram he draw in order to contain it doesn’t work. Valentine is left unharmed because of the power the Mortal Cup has and the demon listens to what Valentine says and even calls him master.
The attention shifts on Jace and Clary. Jace returns to the Institute with Isabelle and Alec after they went hunting for demons only to find that Maryse, Isabelle and Alec’s mother came back. She is extremely cold towards Jace and even sends her children away to talk with him. Maryse then tells Jace that she can’t trust him and that it would be better if he were to leave.
Meanwhile, Clary is with Simon at his house when Isabelle calls her. Clary panics when she finds that Jace ran away and, together with Simon, goes looking for him in the places where she thinks that he will most likely be.
Jace is at a werewolf bar and his presence is noticed by a young girl named Maia. A young werewolf boy is found dead in the alley behind the bar shortly after Jace arrived but he remains indifferent to the boy’s death saying that there is nothing he can do for him. A werewolf named Bat gets angry and he and Jace start fighting. They are stopped by Luke before great damage could be done and he takes Jace into the owner’s office from where he calls Clary.
When Clary arrives at the bar she finds what happened between Maryse and Jace. Luke is shoked to find what Maryse said and offers Jace a place to stay but only if he goes to the Institute and talks with Maryse first. Jace agrees but convinces Luke and Clary to go with him.
When they arrive at the Institute, they find Maryse in the library talking with Raphael about the death of the young werewolf and the death of a fey child that happened a few days earlier. The vampires are suspected because the victims were drained of blood but Raphael denies it.
Maryse recognizes Luke and is surprised to see him. Luke tells her that Jace was not lying and that he wasn’t a spy for Valentine. Luke suggests that Jace to be tested with the Soul Sword to be sure that he is telling the truth and that they should announce the Inquisitor. Maryse reveals that The Inquisitor is already on her way and she thinks it would be better if Jace were to run away because the Calve will most likely judge him and strip his Marks.
Jace is asked what he wants to do and he decides to stay at the Institute and face the Inquisitor.
Simon, Clary and Luke return to Luke’s house. Clary receives her mother’s stele as a present for Luke. Maia comes over and Luke hopes that she will bond with Clary. Simon remains overnight and he and Clary go to sleep.
Jace is woken up from his nightmare by Alec who takes him to the library. Maryse and the Inquisitor, Imogene Herondale, wait for him inside. The Inquisitor starts criticizing Jace and accusing him of being Valentine’s spy. Jace talks back to her and she decides that Jace will be sent to spend the night in the prison under the Silent City, believing that it will teach him some respect.
Jace is taken to a cell and bound with cuffs and left alone in the darkness. Jace starts to hear strange screams coming from above and Brother Jeremiah comes running to his cell only to collapse and die in front of it.
Jace reaches for the troche Brother Jeremiah dropped and tries to see what could have killed Jeremiah but he passes out after something attacks him and blows out the torch.
When Jace wakes up, his father is sitting in front of his cell with the Soul Sword in his hands. He refuses to let Jace out and leaves after he hears strange noises from upstairs.
Isabelle, Alec and Clary arrive at the Silent City. After Isabelle called Clary to tell her that Jace was taken to the Silent City, she went to the Institute. While she was there, the Silent Brother asked for help and they decided that they must act.
They found all the Silent Brothers dead and Jace passed out in a cell. Clary used a rune to break the cell and they left with Jace who told them that Valentine came and that he killed all the Silent Brothers and took the Sword.
When they reached the surface, they found at the entrance about twenty Shadowhunters, with Maryse and Imogene leading them. Alec explained that they answered a call from the Silent Brothers but Imogene was mad at them for taking Jace out of cell and insisted that he has to be taken back.
Isabelle insists that Jace needs medical attention and that Magnus Bane can help him. Magnus appears out of nowhere and agrees to take Jace to his apartment and take care of him. Imogene agrees but only is Magnus will make sure that Jace will not escape.
A few days after the incident, Clary and Simon go to Magnus to see Jace. He tells them what happened and Magnus believes that there is a link between thekilled Downworlders and the stolen sword. He concludes that maybe Valentine wants to change the sword so that it will have a demonic power and that it will be easier that way to control and even summon demons. In order to do that, he has to seethe the sword into the blood of four Downworlders.
Alec calls his mother and tells her their theory. He then informs the others that Isabelle told him that the Seelie Queen requested their presence and that it might be wise to go and see her because she might become an ally against Valentine.
Alec remains in Jace’s place at Magnus and them Simon, Jace and Clary meet with Isabelle at a pond. They go into the water and then they are taken underground. They meet with a knight at the court and he takes them to the Queen.
Jace warns them not to eat or drink anything that they are offered before continuing.
They are taken in front of the Queen and at first she refuses to help them. When they get ready to leave, The Queen tells them that Clary must stay because she drank from what they offered when she took a rose petal from the drink and hurt her finger. She put her finger in her mouth and thus consumed their drink.
The Queen agrees to let her go but only if she is kissed by the one her heart desires the most. Jace kisses her and they are brought back to the surface by the same knight.
Once outside, Simon leaves without looking at them and doesn’t stop when Clary runs after him. Knowing that they won’t catch him, they return to the Institute to change out of their wet clothes.
Clary goes to Jace’s room and he shows her a piece of the portal. They talk about their feeling but reach the conclusion that they can’t be selfish and continue a relationship that goes beyond a normal one between a sister and a brother.
Jace goes to shower and Clary remains alone in his room. She falls asleep and dreams about Jace being an angel and Simon having bloodied wings. She wakes up with Jace beside her.
The Institute’s doorbell rings and they find Raphael with a badly injured Simon in his arms. He tells them that Simon is not dead yet but he will be if they don’t burry him so he could rise as a vampire. Apparently, Simon went to the vampires’ lair and because he still had vampire blood in his system he will become one too.
Clary rushes them to the Jewish cemetery so they could burry Simon before the sun rises.
Raphael goes with them and he digs Simon’s grave. Alec and Magnus come with animal blood bags and they wait for Simon to rise. When Simon comes out of his grave, Clary rushes to his side but he attacks her. Raphael takes Simon off her and he gives him some of the blood bags that were brought. Not being able to see her boyfriend in that state, Clary runs downhill and passes out.
A few days later, Clary sits by her mother’s bedside in the hospital telling her what happened. Luke comes in and assures her that she shouldn’t blame herself for what happened.
When they arrive home, they see Simon on the doorsteps waiting for them. Luke gives them some time alone to talk things over. He returns however shortly with a wounded Maia in his arms and Clary sees that he ran a demon over in the driveway.
Luke thinks that the demon was sent after someone and that Maia got in his way. Because Maia was wounded, Luke sends Clay and Simon in the kitchen while he cleans her wounds to call the Institute and ask for help.
After calling Jace, Simon returns to the living room to stay with Maia while Luke moves the truck from the driveway. When Simon touches her, Maia realizes that Simon is a vampire and is ready to attack him. Clary comes and stops them by jumping between them on the table.
Jace, Alec and Magnus come in and Jace gets mad at Clary when he sees her on the table. Magnus starts healing Maia and when he asks about Luke, Clary becomes worried. Simon, Jace and Clary go outside to look for him and they see a demon dragging him away. They scare the demon away and bring Luke into the house. Magnus heals him too and they all remain at Luke’s house except for Simon.
After everyone falls asleep, Jace goes outside and meets with Raphael who gives him a vampire motorcycle. Jace flies over the river where he notices a black ship. He lands on it and goes under the deck where he sees Clary wounded. He passes out shortly after that as is woken up by Valentine.
When Jace is asked how he found the ship, he confesses that he tortured the demon Valentine sent to Luke’s house and that it told him where to find him. Valentine takes him outside and shows him the demon army that he gathered and reveals his plan to destroy the Clave. Valentine promises Jace that he will not hurt those he loves but only if he is willing to join him.
Meanwhile, Clary wakes up at Luke’s house and she goes to the kitchen where she finds the others. They ask her about how she managed to fight off the demon the previous night and she told them that she must have scared it off. She showed them a rune she draw on herself and no one knew what it meant.
Clary believes that she can create new runes and they try this theory by putting her to draw a rune signifying fearless. Alec offers to try the rune and see if it works but he doesn’t notice any change after Clary puts it on him.
Maryse, her husband and Imogene come to Luke’s house where Imogene starts to yell at Magnus for letting Jace meet his father. Alec almost confesses that he is seeing Magnus but is stopped before he could say anything.
The Inquisitor takes the piece of portal from Jace and breaks it revealing a piece of paper with a rune on it that helped her track Jace. Because Jace broke the law, The Inquisitor decides that she will take him to Idris the next day. Jace is taken from Luke’s house and runes are put on his wrists to prevent him from running.
Clary and Luke talk about Jace after the other left and even if Luke suggested that they leave, Clary refuses to go without Jace. Maia, who remained at the house, ran off shortly after Jace was taken away. She wondered aimlessly until she was cornered in a dark alley by someone who looks like her dead brother, Daniel. He is stopped by Valentine and he takes Maia away.
Meanwhile, Jace is taken back to the Institute and separated from the others. The Inquisitor takes him to the weapons room and puts him in cage made by runes. Jace finds that the Inquisitor wants to trade him for the Mortal Instruments. Jace tell her that Valentine will never accept this but she refuses to believe him.
After Imogene left, Alec comes in. He brings Jace a device that helps his take the runes of his arms and frees himself. Alec suggests that maybe he has some special abilities just like Clary and that he could free himself from the cage. Looking upwards, Jace sees that the cell has no ceiling and he prepares himself to jump.
After Clary and Luke notice that Maia disappeared, they call Simon’s house hoping that she would go there. She is however not at Simon’s and shortly after Clary calls him, something tries to break into Simon’s house.
Luke and Clary rushes there but the call gets disconnected before they arrive. When they reach Simon’s house, he is nowhere to be seen and his phone is on the ground, containing a message from Valentine telling them that now he has them all. Luke thinks that maybe Jace made Valentine mad and that pushed him to take Simon and Maia instead of taking some random werewolf and vampire children.
Back at the Institute, Alec tries to convince Isabelle to let him in her room to talk but without results. He enters however and Isabelle is mad at him because she thinks that he betrayed Jace. After a few moments Jace also comes into the room and he takes some of Isabelle’s weapons and sends Max, Isabelle and Alec’s younger brother after Isabelle’s phone so he could talk with Clary.
Jace finds that Simon and Maia have been abducted and he tells Clary to come at the Institute after him. When they arrive at the Institute, Jace is on the rooftop and he jumps, landing perfectly in front of the car. Together they start driving towards the river where they meet with Magnus who puts a spell on the truck so it hovers above the river. Jace asks Clary to draw the fearless rune on him so he could fight the fear demon their father has.
even after he figures out what Valentine plans to do with them. When Valentine comes in, he throws silver dust at Maia and then asks Simon if he has anything to say before he will kill him. When Simon says Clary’s name, Valentine gets angry and slashes the Sword against Simon’s neck.
Back at the Institute, Alec and Isabelle listen at the Library door but hear nothing. When they enter, they find the Inquisitor and their mother looking with hate at each other. An image with Valentine appears and he makes it clear the he will not trade the Mortal Instruments for Jace because he already chose not to join his side.
The Inquisitor is surprised to hear that Jace was not controlled by Valentine and realizes the mistake she made. Robert Lightwood appears in the room and tells them that they don’t have time to wait for the Clave to send reinforcements and that they should go after Valentine and stop him with the Shadowhunters they have.
In the back of the truck, Jace kisses Clary before preparing himself for battle. He tries to convince her to stay in the truck but they are attacked by demons and one of them takes Clary and flies away. Jace and Luke go after her while Magnus remains in the truck. When they get on the ship, they are immediately surrounded by demons.
Clary ends up under the deck and finds Maia still alive. Maia tells her that Simon was killed by Valentine and that he will come after her too. Clary breaks the wall using her stele and then Maia goes through it. When Clary is ready to pass on the other side, Valentine catches her and takes her away in another room, telling her that he will trade her for Maia.
Outside, Jace and Luke are outnumbered and they have no more weapons left. They are saved by the other Shadowhunters coming to their aid. Jace is saved by Imogene but she dies trying to protect him. Isabelle is also hurt and while Alec tries to get her to safety, the deck collapses and takes Jace with it.
Inside the ship, Jace wakes up on a narrow catwalk. . He starts looking around and realizes that a figure that looks like his father is standing on the other side. Valentine tells Jace that it is his fault for everything that happened, that Clary is hurt because of him and that every death rests on his shoulders. Jace refuses to believe that he is turning into his father no matter how many similarities exist between them and he stabs Valentine with a piece of metal. Valentine turns into dust and Jace knows that it was a demon and not his father.
Jace finds Simon in a room and at first he believes that he is dead until he notices that he is still breathing. Jace feeds Simon his blood and after he wakes up they go looking for Clary. When they find her, Jace and Simon start fighting with Valentine while Clary is thrown on the other side of the room. Jace throws her the stele belonging to their mother and Clary draws a rune that destroys the whole ship.
Clary wakes up in the back of Luke’s truck with Simon and Jace by her side. She finds that the rune tore the ship apart and that Valentine must have run off because neither he nor the Mortal Instruments could be found. Some Shadowhunters were killed but none as a result of Clary’s rune.
They watch as the sun starts to rise and Clary looks with fear at Simon, knowing that he will burn. However, when the sun comes up, Simon remains just the same, unaffected by sunlight.
Back at the Institute, Jace packs his belongings when Maryse comes into his room. She tries to persuade him to stay at the Institute and confesses that he is the only one who is not related through blood with her that she ended up loving.
A few days later after the incident, Clary goes to Simon’s house. They break up reaching the conclusion that it is better if they remain friends. Clary also meets with Jace and he agrees with her regarding their relationship saying that it is better if they remain just brother and sister.
Clary leaves Jace and goes to the hospital. Outside, she sees a cloaked figure hidden by glamour. The woman introduces herself as Madeleine Bellefleur and she tells Clary that her mother did that to herself and that she can help her.