After Clary met with Madeleine, she runs to tell Jace the good news. However, he doesn’t like the idea of her going to Idris. Maryse overhears the conversation and offers to take Clary with them since they are going for an official Clave meeting. Jace is furious, but Clary refuses to not go considering the warlock, Ragnor Fell, is expecting her and will most likely refuse anyone else. Clary is in the process of packing when Simon stops by before heading off to meet Maia. Luke brings Clary a green coat that will help her fit in with the Shadowhunters. He is not happy that she is going to Alicante without him. Simon arrives at the Institute because Jace asked him to talk. The Shadowhunter asks him if he will tell the others that Clary changed her mind about going. He has already told Clary the wrong time to show up to go through the temporary portal Magnus is creating. Forsaken arrive and attack the others. Jace flings himself into the fist and so does Simon when he sees Isabelle attacked. They all go through the portal to get away, including Simon, who is dragged by Jace.
Luke takes Clary to the Institute. She goes ahead of him to find the building completely shut down. Magnus finds her and explains what happened earlier, including Madeleine’s death. Clary wants him to reopen the portal for her, but the warlock explains that there are wards around the city; they would have to know that she is coming for it to work. Clary is upset and storms off. She finds the spot where Magnus’ portal was and draws a rune to create her own. She thinks of the ballroom in Alicante she dreamed about just as Luke finds her. She goes through and pulls him through when he tries to stop her. Simon wakes up in a strange bedroom with Isabelle sleeping in a chair next to his bed. She wakes up and reminds him what happened back in the Institute’s garden. Jace comes in and tells him they had to explain to the Clave why they brought a vampire to Alicante. Simon realizes that he has lost blood from the stab wound and needs to replenish it. Jace sends Isabelle out before giving Simon juice he squeezed out of raw meat. Simon is not happy to be there and’t wouldn’t be if Jace had not wanted to keep Clary from coming. Jace points out that he has broken the law to save Simon on multiple occasions, this being one of them. Isabelle interrupts to let Jace know that Alec is going up to the Gard and wants to talk to his paraboti about Simon before he leaves. Simon insists on being there if they are going to talk about him. Clary and Luke are spit out of the portal and into Lake Lyn. Luke drags her out and tries to make sure she spits out any water she might have ingested. He is furious at her tantrum about being left behind. They start the long walk towards Alicante. On the way, Luke tells her that the Angel Raziel came out of Lake Lyn to give the Shadowhunter the Moral Instruments. The lake has been cursed since and the water is poisonous to Shadowhunters. As Simon sits with Jace, Isabelle, Alec, Aline and Sebastian, they tell him about the third Mortal Instrument, the mirror, which no one has seen for hundreds of years. Isabelle also explains how the Bone City isn’t actually in New York, that is just were one of the many entrances is located. Aline changes the subject away from Shadowhunter secrets and onto Simon. When the focus shifts again, Sebastian explains his parents were killed by demons. Aline had been looking forward to meeting Clary, and Jace says she didn’t want to leave New York. Simon is about to tell the truth when Jace pulls him out of the room forcefully.
Luke leads Clary through Idris towards Alicante. When they get to a cemetery, they start going through and Clary sees the Fairchild mausoleum. Her mother’s name is on it. clary turns to see her own grave and screams. When she looks again, it is gone. Luke says they must hurry because the hallucinations from the lake water have set in. Jace scolds Simon for almost telling the others that Clary wanted to come. Simon agrees to lie to them if Jace is willing to convince Clary he doesn’t have feelings for her. Jace explains that he already has. Simon asks what Valentine said after Clary drew the rune on the ship. Jace explains that Clary signifies a change in the Shadowhunter race, a war between two sides that will result in a new world for the winner. Luke sneaks Clary into the city through the woods. She starts hallucinating that he is in his wolf form and starts screaming. He gets her to Amatis’ house, who tries to turn him away. He explains that Jocelyn’s daughter is dying. She allows Luke to bring clary inside. Simon is left out of the conversations between Shadowhunters. Jace’s flirtations with Aline makes Simon uncomfortable. Alec returns to get Simon because the Clave has decided to send him home. Jace seems suspicious and tells Alec to make sure that happens.
On the way to the Gard, Simon tries to connect with Alec with the one thing they have in common: unrequited love. When they arrive, Consul Malachi is not at all pleased with the situation. Inquisitor Aldertree sends Alec away, promising that Magnus Bane is waiting to receive Simon in New York. The young Shadowhunter is suspicious. The Inquisitor takes Simon while Consul Malachi shows Alec out. Luke and Amatis take care of Clary. When she wakes up, she drinks some sort of medicine that Luke gives her. He introduces her to his sister, Amatis Herondale. Inquisitor Aldertree asks Simon how he became a vampire. Simon tells him the story, but leaves out the parts that might get his Shadowhunter friends in trouble. The Inquisitor claims that he is lying and has the vampire thrown in a cell. The man in the next cell over explains it took them a long time to fix the cell to hold a Jewish vampire. Jace is waiting for Alec when he returns. Alec tells him that he left Simon with the Inquisitor. Jace is furious and points out the Clave’s mistakes. After he goes inside, Alec writes a letter and sets it on fire with a rune.
Amatis brings clary food and tells her about her experience with Valentine and the Circle. Clary asks about Luke. Amatis says that he went to see his old wolf pack and would be back in a few days. Clary wants to go see Jace and find Ragnor Fell. Amatis tells her that she needs to lay low because she and Luke broke the law by coming there. Clary agrees and Amatis leaves her to rest. She goes through some old clothes until she finds old Shadowhunter gear. Clary puts it on and climbs out the window. The Inquisitor has Simon brought out of his cell to make him a deal. he wants the vampire to confirm a story saying the Lightwoods have been in league with Valentine. Simon refuses and is sent back to his cell. After getting herself lost in the city, Clary asks for directions, which doesn’t seem suspicious because Shadowhunters are visiting from all over the world. When she knocks on the Penhallow’s door, Isabelle answers. Simon has a conversation with his cell neighbor, Samuel. The man says he knows about him, the Daylighter, from the guards gossiping. He tells his story and explains that he is more afraid of Valentine than the Clave. Isabelle tries to convince Clary to go home, but she refuses. She gets past Isabelle, who yells for Sebastian to stop her. He does, but Isabelle eventually decides to let Clary do what she wants. Upstairs, Clary finds Jace in a passionate embrace with Aline.
Jace is furious with Clary for coming to Idris. He sends Aline out of the room and Alec comes in trying to tell Jace something important. Jace tells Clary that he didn’t want her in Idris because there is a war coming and she will mess everything up. She leaves, telling him he is just like Valentine. Simon explains the Inquisitor’s proposition to Samuel, who admits he’d take it to save his own skin. He also points out that they might kill him anyway. simon tells him that his loyalty to the Lightwoods is really because of Clary. Alec is finally able to tell Jace that Magnus never received Simon. He overheard the guards talking about the vampire brought by Valentine’s son. Jace is furious again and punches a hole in a large picture window. Clary runs out of the house and starts wandering the streets of Alicante because she can’t remember how to get back to Amatis’ house. Sebastian catches up with her and offers to walk her home. He swears on the Angel that he won’t tell anyone where she is staying. Instead of using a healing rune, Alec bandages Jace’s hand. He asks why he lied to Clary about how he feels. Jace points out that Alec lies to himself about being in love with him to avoid a real relationship with Magnus. Jace asks Alec to tell the others that he is sick upstairs while he goes to free Simon. Clary and Sebastian talk about their families as he walks her home. His parents were killed when he was very young and was raised by his aunt. He wishes he had older siblings that could tell him about his parents, but he was an only child. When they reach Amatis’ house, they part and clary climbs back in through the window. Amatis is waiting for her. She tells Clary how badly she treated Luke when he though he might turn and is afraid she will disappoint him again. Alone in the guest room, Clary realizes that everyone is mad at her because of her selfish actions.
Jace goes to free Simon from his cell. However, Simon tells him what he knows about the Inquisitor’s plan to blame the Lightwoods. Simon asks Jace to bring him animal blood so that he doesn’t give in. Sebastian comes to tell Clary that he found Ragnor Fell. She agrees to go with him and they set out on horseback. When they arrive, Clary is disappointed to find Magnus instead. The warlock freezes Sebastian and tells Clary what is going on. Valentine found Ragnor, who left a note for the next warlock that found him dead. Magnus tells Clary that she needs the Whitebook, which her mother hid in the library of Wayland Manor. She’ll need Jace’s help to get past the wards. Magnus agrees to make the antidote in exchange for the book. Clary agrees. She tells Sebastian that they are leaving without help. He takes her to the charred remains of Fairchild manor. He kisses her and she doesn’t feel right about it. He wants her to admit they have a connection, but she can’t. She calms him down after an outburst and start riding back to Alicante. He tells her about Simon being in the jail in town.
Raphael’s projection appears in Simon’s cell. He tells Simon that he should either be with his kind or leave everything behind and stay hidden. Simon refuses to leave his family and Raphael points out that Simon still thinks he’s alive. Jace is there when Clary returns to Amatis’ house, she leaves them alone to talk. Clary is furious at him and attacks him until he stops her and explains the situation about Simon. Clary explains what she has learned and suggests Magnus might help them get Simon home for the Book of the White. He agrees to take her to Wayland manor to find it. Samuel explains to Simon that Valentine has found a way to get demon blood into the city to take down the wards. Clary creates a portal and she and Jace travel quickly to his old home. When they get to the library, Jace immediately finds the cookbook that hides the spell book they need. Jace points out Valentine’s journals about his son that he wasn’t allowed to read. They start knocking them off the shelves and a secret doorway appears in the wall.
Jace and Clary make their way downstairs into a cellar. They find an Angel, Ithriul, under a sheet and suddenly see visions. Valentine collected blood of a greater demon to give to his son before he is born, which will eventually burn out his humanity. He then summoned and trapped the angel, trying to get answers and taking his blood as well. Afterwards, Clary fixes the runes that bind the angel to let him go. Jace hands him his seraph blade and Ithriul kills himself. The house starts to collapse and Jace and Clary race out. They end up making out in the grass. Clary pushes him away. He admits that he is willing to be with her now because it is something someone part demon would do. Clary, who they suspect to be part angel, points out that she doesn’t have demon blood in her but she still wants him. They start making their way back to the city, but when they get close, they see that it is on fire.
Isabelle is worried about Jace being gone for so long. Aline suggests they go to bed after Max comes down saying he saw someone climb the demon towers that keep the wards for the city. Aline is snatched out of a window by a demon and dragged away. Isabelle runs after her and between the two of them they dispatch of the demon. Aline runs off and Isabelle goes after her again. She is stopped in shock when she sees the streets sees the street swarming with demons. Alec gets her in the house and tells her to wait there while he goes after Aline. Isabelle goes to get her stele to help Sebastian put protection runes on the house. When she gets back, Sebastian and Max are gone. Sebastian calls to her and she follows his voice to the kitchen. He hits her over the head with a hammer. Alec runs through the city searching for Aline. He gets up to a roof and starts running on top of the city. He sees Magnus fighting off Iblis demons and goes to help him. Alec wants to know why Magnus hasn’t called him back. Magnus explains that he loves Alec, but knows it won’t work between them because Alec loves Jace and only comes to Magnus when he needs something. More demons arrive and Alec promises if they live, he will introduce him to his entire family. Magnus agrees to the terms.
Jace wants Clary to wait outside of the city. A giant pack of werewolves goes running past them and he changes his mind. he gives her a seraph blade and they run to the open north gate. They start fighting off a demon and Maia comes along in wolf form to finish it off. They all make it to the Hall of Accords (which is still warded). Alec and Magnus come up to them. Luke arrives and Clary runs to greet him. Consul Malachi starts arguing with him about the werewolves coming into the city to help. Clary uses the opportunity to give Magnus the spell book. Sebastian finds them and drags her off to talk as the warlock, Jace, and Alec watch. He keeps trying to get her alone, and is upset she gave the book to Magnus. He tells her Simon is still in the prison. Jace and Alec come over and say they will take her to get her friend.
Simon is waiting for the fire to get him when Clary shows up. Jace knocks the bars from the window and they get him out. Simon tells them Samuel is also in the next cell. Jace pulls him out and they come to find it is actually Hodge. He explains hat he tried to warn the Clave of Valentine’s plan when he realized he could never be a Shadowhunter again (not even in Valentine’s regime). He tells them that the Mortal Glass is Lake Lyn. Jace asks how much Hodge knew about him, which was not much. Just as Hodge is about to tell them what Valentine will do with all three mortal instruments, Sebastian throws a knife and kills him. He tries to talk his way out of it, but no one believes him. They realize is is Valentine’s spy. Jace attacks, but is thrown aside. Clary and Alec are also no match for him. Simon attacks and Jace wakes up. They are able to fend him off, but he escapes. They return to the Hall to find Sebastian killed Max.
In the days after the battle, Clary and Simon stay with Amatis. Aline comes over to show them pictures of the real Sebastian that his aunt sent. She also apologizes for kissing Jace, she was trying to find out if she liked guys at all. Clary goes to the hall with Simon to tell Luke about Sebastian. Shortly after she does, Valentine’s projection appears in the hall. He tells them that if they don’t swear loyalty to him by the next night, he will bring his army and kill them all. Aldertree makes a scene. Valentine’s projection is able to rip his heart out and kill him.
Clary and Simon go to fill the Lightwoods in on what happened when they return from Max’s funeral. Isabelle is shut up in her room blaming herself and Simon goes to talk to her. Jace walks Clary back to Amatis’ house and notices blood on her sleeve. She says it is Sebastian’s and he takes a blood-soaked thread without her knowing. Isabelle was listening in on the earlier conversation but still feels that Max’s death is her fault. She wants revenge. For now, she is willing to settle for a distraction and grabs Simon. Clary is alone in bed when Jace comes into her room. He tells her that, even though it is wrong, he loves her and wants to spend what might be their last night together. They hold hands and sleep.
Jace goes to Luke to tell him that he has found Sebastian using a tracking rune. He is going to go after him in hopes it will lead him to Valentine. Luke questions whether Jace will be able to kill his father. Jace believes he can. He left notes for everyone else, but wants Luke to know immediately so he can keep it in mind while planning. Clary wakes up and finds a note from Jace explaining his plan and saying goodbye. She goes downstairs to find Amatis in the kitchen with Isabelle and Simon. clary asks to talk to Isabelle alone. She shows her the note. ISabelle expected it, but Clary wants to go after him. Isabelle starts explaining how tortured Jace has been his whole life, and how seeing Clary, the only person he’s ever been in love with, makes it worse. Simon, having heard most of the conversation, comes in to defend Clary. Shortly after, Amatis bring Jocelyn into the kitchen.
Clary is shocked to see her mother. Isabelle steps in front of Clary, demanding to know who Jocelyn is. Clary’s mom explains and Clary lets all of her anger finally come out. She runs past everyone and out of the house. Jace rides the Verlac horse out to the ruins of his old home. He uses the blood soaked thread and the stele he stole from Alec to get a visual idea of where Sebastian is. He takes off. Simon finds Clary sitting on top of a hill looking out over the city. THey discuss what has been going on the past few weeks. Clary pieces together what the angel, Ithuriel was trying to tell her. She races to the Hall of Accords and steps up on the dais to address the Shadowhunters that sent the Downworlders away and plan to agree to Valentine’s terms. She tells them exactly what happened on the ship in New York, but they don’t believe her. She creates a run on herself to make her appear as the person that each of them loves the most. They are all confused and seeing someone different. She tells them she also has a rune that could allow a Shadowhunter and a Downworlder to share their powers and knowledge.
While the Clave discusses what they want to do with the information Clary has brought to light, she waits outside. Jocelyn comes out to explain the full story. She fell in love with Valentine and they married young. Jocelyn found out she was pregnant and they were happy. Shortly after, Luke was lead to the werewolf bite by Valentine because Jocelyn told Luke she heard strange noises in the house at night. She was depressed after Valentine told her Luke killed himself. She started having awful dreams and getting sick. After Jonathan was born, Jocelyn could tell he was a monster. She heard crying coming from the cellar and followed it to find Valentine’s experiments. She learned that she was given demon blood to make their baby a better Shadowhunter (since the affects didn’t work on Valentine). Jocelyn received a letter from Ragnor Fell (family friend) informing her that Luke was still alive. She started acting normal and plotting. She knew Valentine was giving something to Celine Herondale during her pregnancy. She later learned that Celine killed herself (after her husband, Stephen, was killed in battle), and Valentine and Hodge saved the baby, who is now Jace. After Valentine faked the death of himself and Jonathan, he raised both boys separately. Jocelyn tried to keep Clary hidden from Valentine. Luke comes out of the hall to tell them the Clave has agreed to use Clary’s alliance rune.
Jace makes it to the house in the valley he tracked Jonathan to, but no one is there. He tries the tracking rune again, but only gets darkness. Valentine’s bird, Hugo, appears and Jace decides to try following it. Meanwhile, Clary shows everyone how to draw the rune they will be marking each other with. Jocelyn marks Luke first to show the Downworlders that it won’t hurt them. Clary sends Simon to tell the Lightwoods the truth about Jace. Still following Hugo, Jace ends up in a cave. When it splits into two tunnels, he hears voices down one and follows them. Alec searches the crowd for Magnus while Simon tells the Lightwood siblings about Jace. Alec leaves them, partners up with Magnus, and then kisses the warlock. Many people around them are shocked, including his parents. Simon is awkward around Isabelle and Maia. Raphael projects himself into the hall. He says the vampires will join the battle if they can have Simon. Jace comes to a man made cavern int he tunnels. Valentine and Jonathan are there. Simon overhears Luke, Jocelyn, and Clary all refuse to give up Simon to have the vampires fight with them. Jace listens in to Valentine’s plans. He is confused by fake-Sebastian’s name being Jonathan. Once Valentine leaves for the lake (leaving Sebastian to summon the demon army at midnight), he acknowledges Jace’s presence. Jace thinks they are brothers. As Clary makes her way through the crowd, Simon pulls her aside. He wants to give himself up to the vampires so that they will agree to fight with the others. After he explains his plan in full, Clary draws the first mark on his forehead with a stele.
Maia takes Simon out of the city and to the vampires. he tells her to leave so they don’t both die. She does. As Raphael gets ready to kill him, Simon shows him the Mark of Cain; anyone that tries to hurt Simon will suffer seven times worse. Raphael still agrees to fight with the Shadowhunters if Simon fights with them. Jace wakes up tied to a stalagmite with blood in his mouth. Sebastian releases the demons to attack the Clave early. He repeatedly points out how he is Valentine’s sone and hints that Jace is not. Jace tries to convince him that Hugo will inform Valentine if Jonathan kills him while he’s tied up. He lifts his sword and brings it down. Clary is sitting in the Hall of Accords when the demons are released. The skylight rains down on her as the demons pass. Simon and the other vampires are almost to the battle field when it happens. Jace wakes up outside in the valley. Sebastian comes at him with a sword, but Jace only has a small dagger. Jace is able to fight him off for a while, but ends up on his back. Sebastian is above him with his knife over Jace’s heart. He explains that Jace was never Valentine’s son. Jace feels the knife starting to go into his chest and can’t move. When Sebastian lifts the blade to finish Jace, Isabelle appears and cuts off Jonathan’s hand with her whip. He leaves Jace for dead and goes after something to stop the bleeding. Isabelle starts an iritze (healing rune) on Jace, but Sebastian comes back for her. Jace gets up and grabs the dagger. THinking of Clary gets him close enough to put the dagger into Jonathan’s back; into the spot that Valentine told him would pierce the heart and sever the spine. Jace collapses. Simon makes it to the battle. He doesn’t even start to fight before a Shadowhunter saves him, and then is swept away by a demon. Simon starts attacking a demon nearby. Clary decides to leave the hall and join Aline. She is almost out of the hall when Consul Malachi comes in for a private place to contact Valentine. He tells his leader about Jace going after him and fighting his real son. When clary gets over her shock, she hears them talking about turning Shadowhunters into forsaken. As Malachi starts to leave, Hugo points out Clary. Malachi stuns the bird before going after her. The bird saves Clary and kills Malachi on the glass from the shattered skylight. Clary races for the portal.
Clary lands in the lake again. Valentine pulls her out and cures her of the poisonous water before binding her to be the sacrifice for the ritual to call the angel. Just as Valentine is about to kill Clary with the Mortal Sword, Jace appears. He is ready to kill Valentine with Sebastian’s sword, but Valentine is faster. He drives the Mortal Sword into Jace’s chest and then holds him until he dies. He then goes to the lake and puts the blood soaked sword in it, chanting. He throws in the cup. Clary wants to go to Jace’s body, but instead she crawls over to the ritual runes Valentine has drawn. She changes the rune that means her father’s name just before the throws the sword into Lake Lyn. The angel rises and Valentine tries to explain the corruption of the Clave. Raziel explains that his judgement is different from heaven’s. Demons don’t have souls, but Downworlders do. Valentine points out that he preformed the ritual. The angel informs him that his daughter is the master of the circle that called him. Valentine is shocked, but before he can plead, the angel kills him. Raziel asks Clary what she wants, and tells her the battle with the demons is already ending. The demons start to leave when Valentine died. She says that she wants Jace. He tells her to close her eyes. When she opens them again, Jace is holding her. He knows that he died and that Clary could’ve had anything, but asked for him. She makes sure he knows they aren’t related.
Jace is released from the hospital after a few days of sleep to attend Valentine’s funeral. He goes away from the crowd and up the hill to watch him burn. Luke comes to tell him it is okay to miss and remember the man who originally raised him. Clary and Aline sit in Isabelle’s room while she decides what to wear to the celebration later that night. Aline wonders out loud if Jace will still want Clary now that their love isn’t forbidden. Isabelle describes how the night will be like a New York street fair that Max would’ve loved. Jace goes to see Clary, but she isn’t at Amatis’ house. She asks him in and gives him a box of his biological father’s possessions. He asks her about the scar on his shoulder that provoked Imogen to save him. She says it is a birthmark that all Herondale’s have. It is supposed to mean that the person was touch by an angel. Clary comes back to Amatis’ house to hear Luke and Jocelyn arguing about Luke staying in Idris to take the werewolves’ seat on the council. She tells him if he wants it, he should take it. He tells her that he loves her and then leaves. Amatis tells Jocelyn to let him go if she doesn’t love him. Clary doesn’t see what happens, but hears Amatis tell her mom to go after Luke. Jocelyn stops in the hallway when she sees Clary, who tells her to go after him. Jocelyn starts running. Amatis tells Clary that Jace came by to see her. Clary asks if she can borrow the dress she found in the spare room. She goes to the Lightwoods and meets up with Isabelle, who tells her that Jace is in the square. they are joined by Alec, Aline, Simon, and Maia and all start walking together. Simon tells Clary that he plans to try for as normal a life as he can. He promises her that when he chooses a girl, he won’t cut her out of his life. She admits she is planning to finish her education at the Institute and will be drawing the symbol for the new council. They arrive in the decorated town square. Clary sees Magnus talking to a girl that seems familiar, but she disappears. Shortly after, Magnus comes over to talk to them. He whispers to Clary to go to the Accords Hall steps. She finds Jace there with the silver box Amatis gave him. He’s wondering who he really is and if he even has a name. Clary points out that the Lightwoods are his family. Maryse gave him the nickname. She asks if he still wants her now that they have the opportunity to be together. He tells her how much he loves her, how she influences him, and how she makes him stronger. He asks if she wants him and she kisses him. Eventually they join their group of friends. From the edge of a small temporary forest, the Seelie Queen beckons to Clary. She goes and the queen asks her to recommend Meliorn for the fairy’s seat on the council. In return, the queen will grant Clary a favor. Clary turns down the offer, saying she has everything she needs and returns to her friends. Jocelyn and Luke find her and look happy together. Luke admits that he is staying in New York and is hoping Jocelyn and Clary will move in with him. They wander off and Clary watches the fireworks with Jace holding her against him.