The narrative begins with Clary and Simon at Luke’s house, a week after they called off their relationship. Clary was packing for a trip to Idris, hoping to find something that will help her mother. Jace was against her going to Idris, considering it to be too dangerous saying that while he and the others were summoned to Idris to take part in the council that will decide what actions will be taken considering that Valentine was back, she had no business there.
Maryse agreed that Clary must go to Idris considering that the clave also wanted to talk with her about what happened during the battle on Valentine’s boat. Jace continued trying to persuade Clary not to go but was unsuccessful. Jace then tried another plan that he hoped will make Clary stay behind. Jace told Clary that they were going to go to Idris at night when instead they were supposed to leave at noon. While Clary was visiting her mother in the hospital, Jace called Simon and tried to convince him to lie and tell the others that Clary changed her mind and decided to remain in New York. Their conversation was interrupted when the group that was supposed to leave for Idris was attacked by forsaken. Magnus opened the portal to Idris and they all ran towards it. Unfortunately, Madelaine was killed and Simon injured, losing his conscious before the battle ended.
Clary arrived at the Institute after the battle ended. She found from Magnus that everyone left and he wasn’t able to open a new portal for her because that would mean that he would break the law. Angry, Clary went outside where she saw the reaming runes from the portal opened by Magnus. She thought about the portal and started drawing a rune on the wall, hoping that she will able to open a new portal. Just before the portal opened completely, Luke reached Clary and they both passed through the portal.
Back in Alicante, Simon woke up to find Isabelle beside him. She told him that he was stabbed and Jace dragged him through the portal, breaking the law that forbidden downworlders to enter Alicante. He meets with two other Shadowhunters, Sebastian Verlac and Aline Penhallow. Jace started flirting with Aline and Simon almost revealed that Clary didn’t stay behind on her own accord before being dragged upstairs by Jace. Jace told Simon that Clary might be in danger because of her ability to create runes and may end up being a target for the Clave if she were to come to Alicante.
Clary and Luke ended up being thrown into lake Lyn, the lake where the legend says that the angel appeared and created the Shadowhunter race. They were a long way from Alicante and Luke worried that Clary may have drunk some of the water from the lake which was said to be poisonous for Shadohunters. Because she lost her stele, Clary was unable to heal herself but Luke was sure that they will find help once they would reach Alicante.
After a few hours, Clary started hallucinating and Luke become more worried about her. They finally reached Alicante and Luke took her to a woman named Amatis before Clary passed out.
At the house where Simon and the others were staying, Alec returned from a Clave meeting to take Simon back so that he could be sent to New York. He took Simon until the meet the new Inquisitor, Aldertree. Alec was told to leave and Aldertree took Simon to a room where he started questioning him about his sire and who transformed him. The Inquisitor also revealed that he didn’t intend to send Simon home and called a group of Shadowhunters to take Simon to a cell. There he discovered from another prisoner that the Shadowhunters have been preparing his cell since that morning, putting special runes so that he won’t be able to escape.
When Clary woke up, she was in a room alone. Amatis came and brought her something to eat and told her that Luke had to leave because he will get in trouble for being in Alicante. Clary expressed her desire to go and see Jace but she was forbidden to do so. Amatis left her alone to get changed and Clary found Amatis’ old Shadohunter gear. She dressed in it and slipped out of the window.
After asking for directions, Clary ended up at the house where Jace was staying and was greeted by Isabelle. Isabelle refused to let Clary pass but she managed to slip past her. Isabelle wanted to convince Clary that Jace was not in the house but Sebastian told her where she could find him. Clary found Jace and Aline kissing in the library.
A few moments later Alec appeared and asked to speak with Jace, hinting that it is something that has to do with Simon. Jace makes him shut up and then proceeds to insult Clary, making her leave the house. After she left, Alec told them that he found out the Simon didn’t reach New York and that he was kept in Alicante for questioning.
Meanwhile, Simon was woken up by a Shadowhunter and taken to the Inquisitor who began asking him about how he became immune to the sun. Simon protected Jace and didn’t reveal that Jace let feed on his blood while on the ship.
The Inquisitor revealed his plan to blame the Lightwood family to make the others trust the Clave again. He told Simon that he wanted to accuse the Lightwoods of being loyal to Valentine and that he needed his help in order to do that. The inquisitor proposed that Simon lie and tell the others that he was associated with the Lightwoods and Valentine and in return, he will be taken back to his family. Simon refused and the Inquisitor ordered Simon to be taken back to his cell. He heard the stranger from the other cell again and found that his name is Samuel Blackburn and that he was a Shadowhunter, loyal to Valentine.
After Clary run out of the house, Sebastian followed her and insisted that he accompanied her on the way back. After they reached Amantis’ house, Sebastian expressed his desire to get to know Clary better but was refused. When Clary entered the house, she found Amantis angry at herself because of her incapacity to do good even when she wanted to. After a brief talk with Clary, she sent Clary to bed while she remained alone.
During the same night, Simon was awoken by Jace who came to rescue him. Simon told Jace about what the Inquisitor thought about the Lightwood family. Jace told Simon that he planned to take him out of Idris but Simon refused, fearing that the Lightwoods will be blamed. Jace insisted that Simon protect the Lightwoods but that he won’t do the same for him, feeling like he deserved to be punished by the Clave.
That morning, Clary was woken up by Sebastian who told her that he knows where Ragnor Fell is and that he can take her to him. They arrived in a clearing and when the door to a small stone cottage opened, Magnus appeared. He froze Sebastian so he could talk in private with Clary. He told her that Ragnor was killed by demons sent by Valentine who was looking for an ancient spellbook, The Book of the White, hidden by Clary’s mother in the library in the Wayland manor. The book also contained the antidote Jocelyn needed but Magnus couldn’t go to the manor because of the wards around it. He told Clary that Jace could enter the manor and get the book. After that, he will prepare the antidote in exchange for the book.
Magnus released Sebastian from the spell and clary convinced him to go back. On their way back to Alicante, they stopped at the ruins of the house where Valentine used to live with Jocelyn. There, Sebastian kissed Clary but she refused him, feeling like something is wrong. Before they went back, Sebastian told Clary about Simon, not knowing that Jace didn’t reveal that he was still in Alicante.
The next day, Simon woke up to find a flask with blood from Isabelle. Shortly after, Rafael appeared in his cell, under the form of a projection. Raphael warned Simon that he will be hunted by other Downworlders because of his ability to walk in sunlight and that he should stay away from everyone he knows for a while.
After Clary arrived home, she was told that Jace was there to see her. Clary got mad at him and Jace ended up telling her about what the Inquisitor wanted to do. Clary told him about the Book of White and Jace agreed that they must get the book before Valentine gets it.
Clary opened a portal and took Jace to the Wayland manor. They quickly found the book and while they were looking through the other books, a dark passage opened. They found cells as they descended, and in one of them, an eyeless angel was bound. Clary entered in a dream-like state, being transported years ago and she saw Valentine being offered blood from a demon so he could give it to a child that will acquire greater powers. The vision shifted and Jocelyn appeared, claiming that she can’t love a child that was transformed into a monster.
The vision ended and Clary realized that it wasn’t the first time the angel showed her that kind of dreams. Clary changed the runes around the angel to release him and Jace gave him a seraph blade. Almost immediately, the angel stabbed himself and burst into flames. The manor around Clary and Jace started collapsing and they barely made it out alive.
Outside, Jace revealed his true feelings towards Clary and that he loves her more than just a sister. They started kissing but Clary stopped him, knowing that it was wrong and that it will end up hurting the people close to them. They started walking towards Alicante as Jace’s stele was lost while the manor collapsed and they managed to reach the city before the sunrise, only to see it in flames.
A few hours earlier, just as Aline, Isabelle, Alec, Max, and Sebastian were ready to go to bed, the city was suddenly attacked by demons that managed to get past the demon towers. The city was left unprotected as most of the Shadowhunters that were able to fight were taking part in a meeting. A demon snatched Aline but Isabelle saved her. Alec found Isabelle in the streets and took her to the house where he felt her with Max and Sebastian while he went to help the others. However, things went south when Sebastian attacked Max and Isabelle with a hammer.
Meanwhile, Alec was traveling through the city by using the roofs to avoid the demons when he noticed that Magnus was in Alicante, also fighting demons. Alec went to him and helped him and expressed his anger that Magnus didn’t answer his calls. Just when Magnus was telling Alec that he was also disappointed that he never admitted his feelings, a group of demons appeared. Alec made a bet with Magnus, telling him that if they survive, he will introduce him to his entire family.
Clary and Jace were looking at the burning city when a big pack of wolves appeared. Jace feared that they were going to attack them but instead they started running towards the city. Jace and Clary also started running towards the city, passing numerous dead bodies.
A demon got out of a destroyed shop and attacked Clary and Jace. They were saved however by Maia, who told them that Luke gathered many packs of werewolves and brought them to Alicante, knowing that the Shadowhunters will need their help. They headed towards the Accords Hall, finding out from Maia that everyone was gathering there because the place was heavily guarded.
There, Alec told them that Isabelle was still at the house with Sebastian and Max and that their parents went after them. Simon was still absent and no one knew what happened to him. Before Clary could ask more about it, Luke appeared in the hall. The Consul was mad at him but Luke insisted that the Shadowhunters needed the Downworlder’s help to fight off Valentine.
Clary talked with Magnus and she gave him the Book of White before Sebastian appeared. Alec was mad at him for leaving Isabelle and Max alone. Sebastian took Clary a bit far away from the others and told her that Simon was left in the Guard and that he can take her there. Jace refused to let her go alone with Sebastian and offered to go with her. Clary chose to go with Jace and Alec while Sebastian left upset.
When they reached the prison, everything was on fire. They managed to get Simon out and he told them about the person in the cell next to him. When they got him out, they discovered that it was Hodge. He told them that he came to Idris to warn the others about Valentine but no one listened to him. He also told them that Lake Lyn was the last of the Mortal Instruments before being killed by Sebastian. When asked why he did it, Sebastian started insulting everyone and revealing that he was actually a spy before attacking everyone. He suddenly ran away and everyone returned to the Accords’ Hall. After they arrived there, they saw Isabelle with her parents and the dead body of Max.
After the attack, Clary and Simon remained in Amatis’ house. Aline came to visit her and brought some pictures of Sebastian from which turned out that the Sebastian they knew wasn’t the real Sebastian. Clary and Simon went to Luke and told him what they found out when a projection of Valentine appeared in the room, scaring everyone. He told them that if they don’t obey him, he will come with a bigger army and destroy every Shadowhunter. Before he left, he killed the Inquisitor.
A few days later, the funerals for the Shadowhunters killed by Valentine took place. Clary, Alec Simon, and Jace discussed Sebastian and what may be his next move and about Isabelle who hasn’t left her room. Simon offered to go and talk to her while Jace took Clary home. Once they reached Amatis’ home, Jace saw blood on Clary’s sleeve and she realized that it was Sebastian’s blood. Jace managed to take a tread from Clary’s sleeve before she went inside.
Meanwhile, Simon managed to convince Isabelle to let him in her room. Simon tried to convince her that it wasn’t her fault that Max died but she continued to blame herself. Suddenly, Isabelle grabbed him and threw him on her bed, saying that she knows one thing that will help her.
After a few hours, when Clary was asleep in Amatis’ house, she was woken up when Jace entered her room. He confessed one more time that he loves her more than just a sister and that he wants to stay with her that night, not knowing what would happen after Valentine would attack the next night. They fell asleep together, holding hands and feeling at ease.
Jace woke up before Clary did and went to see Luke, telling him that he knows how to find Sebastian and that he plans to try to kill him and Valentine. Even if Luke wasn’t too happy to hear his intentions, he realized that he won’t be able to stop Jace so he let him go.
When Clary woke up, she found a note in which Jace explained what he was going to do. When she went down in the kitchen, she found Isabelle cooking while Simon and Amatis watched. Clary showed Isabelle the note Jace left and Isabelle blamed Clary for this. They were interrupted by an unexpected visitor, Clary’s mother.
Instead of hugging her, Clary got mad at her and started asking her why she never revealed the truth about her father and brother before storming out of the house and running away. Simon found her a few hours later on a hill overlooking Alicante and they figured out that the clave refused to work with the Sownworlers and surrender themselves to Valentine when the gates didn’t open for the Sownworlders coming towards Alicante.
Clary rushed towards the Accords Hall, hoping that she will be able to convince them otherwise. Clary told everyone about her power to create new runes and explained to them that she could bind Shadohunters to Downworlders in such a way that they would share each other’s abilities.
Clary was made to wait outside while the Clave deliberated. Her mother came out and insisted on telling her the truth about her and Valentine. She told Clary that Valentine spoke to her when she was in a coma and told her that he experimented on Jonathan by giving him demon blood, hoping that it will make him stronger. Then, he started putting angel blood into Jocelyn’s food as a way of making her feel better and without realizing g that Jocelyn was pregnant. Clary also found that Sebastian was actually Jonathan and that he most likely used his own blood to take down the wards. When Clary asked about Jace, she found that they were not related and that he was the son of Céline and Stephen Herondale. Valentine gave Celine a mixture of angel blood so Jace was also affected. Unfortunately, Stephen was killed during a raid and Celine, who was eight months pregnant, committed suicide. Valentine saved the baby and raised it separately from his trueborn son.
After Jocelyn ended her explication, Luke came out and told them that the Clave decided to let Clary mark them. Some of the Downworlders were suspicious, believing that the rune will either kill them or make them go mad. Clary proved that this wouldn’t happen when Jocelyn marked Luke in front of everyone.
Simon ran to Isabelle and Alec to tell them about Jace’s true parentage and how the new mark works. Isabelle wanted to be partnered with Simon but Alec forbade her, saying that she is not yet an adult. Alec went to find Magnus so they would be partners and Simon, Isabelle and Maia watched as Alec marked Magnus and then kissed him in front of everyone, ending up revealing his feelings and sexuality in front of his parents and other Shadowhunters.
Clary was told that she would remain in the city even though she disagreed. Suddenly, a projection of Raphael appeared, demanding Simon in exchange for the vampires’ help. Jocelyn, Luke, and Clary refused to give Simon up, not knowing that Simon was hidden behind a pillar and listened to every word they said. He managed to get Clary alone and tell her that he plans on accepting Raphael’s terms. Clary drew on him the first mark, the mark of Cain before Simon left.
Jace managed to find the clearing where Sebastian was supposed to be and Valentine’s raven confirmed his suspicions that it was the right place. He started following the raven until he heard hushed voices. Those voices were revealed to be Valentine and Sebastian talking about how they will summon Raziel at lake Lyn. Jace tried to run and go warn the other but was stopped by Sebastian who knocked him out.
Meanwhile, Maia took Simon to Raphael. When he saw him, Raphael was ready to kill him but stopped once Simon showed him the mark of Cain on his forehead. Even though he couldn’t kill him, Raphael decided that Simon was to fight alongside the other vampires in the battle against Valentine.
When Jace woke up, he was tied up and Sebastian was getting ready to summon the demon army. After he released the demon army, he went towards Jace with the intent of killing him. Jace tried to persuade him to untie him so they could have a fair fight and Sebastian agreed. The fought for a while but Sebastian won, stabbing Jace through the heart. Before he died, Jace found that he wasn’t valentine’s son and that he had angel blood in him. Isabelle appeared in the last moment and cut one of Sebastian’s hands off before he managed to run away. Isabelle tried to heal Jace with a healing rune but was stopped when Sebastian appeared again and started attacking Isabelle. Jace found his strength to kill Sebastian before collapsing once again.
The demons passed over Alicante and then attacked the Shadowhunters and the Downworlders on the battlefield. Simon was fighting too and saw all the Shadowhunters he knew fighting against demons. Clary heard Malachi talking to Valentine about how his two sons were fighting and she realized that he was loyal to Valentine. Malachi discovered Clary listening and was ready to attack her when he was killed by Valentine’s raven. After that, Clary rushed towards the portal.
Clary was thrown once more in Lake Lyn and the one who pulled her out was Valentine. Clary saw the altar made by Valentine where he wanted to summon Raziel. Valentine almost killed Clary when Jace appeared. He was however killed by Valentine, who trust the Mortal Sword in his chest. After that, he went towards the altar and begun summoning Raziel. Not wanting to just stay and watch, Clary crawled to the runes made by Valentine and changed them slightly. When Raziel appeared, he refused to grand Valentine’s request, saying that he owns a request but to his daughter. The angel killed Valentine and then asked Clary what was that she wanted. She only said Jace’s name and fainted. When she woke up, Jace was beside her, alive and well.
A few days later, Valentine’s burial was being held. Jace was watching from a distance but Clary was absent. He went to Amatis’ house, believing that Clary will be there but she was with Isabelle. Amatis gave Jace a box with some of his father’s belongings, saying that if one day he will have questions about him, Jace can find a few things about his father from his belongings.
When Clary returned home, Jace was already gone and Jocelyn and Luke were talking in the kitchen. Luke confessed his feelings for Jocelyn and after she didn’t said anything, told her that he will remain in Alicante as a council member. Amatis and Clary persuaded Jocelyn to run after Luke and confess her true feelings for him.
That night, everyone was celebrating their victory against Valentine. Magnus told Clary where to find Jace. He was confused on who he is, feeling lost as he didn’t felt no connection with his father’s belongings. Clary told him that he was a Lightwood and they both agreed to start again their relationship.