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As the Lightwoods, Jace and Clary prepare to leave for Alicante, the Institute is attacked by Forsaken, forcing the others to leave without Clary, and take Simon with them.

While the others meet up with Aline and her cousin Sebastian, Clary, stranded in New York, creates her own Portal to the city and travels there with Luke. They arrive in Lake Lyn, where the cursed water makes Clary feverish, and Luke takes her to his sister Amatis to recover.

Alec is ordered to bring Simon to the new Inquisitor, who wishes to know why a Downworlder is in Alicante. Under the ruse that Simon is being sent home, the Clave secretly interrogate and imprison him.

Clary sneaks out to visit the Lightwoods, but argues with Jace and storms out. After leaving, Clary meets Sebastian, and tells him about her mother's coma and her need to find the warlock Ragnor Fell. Sebastian takes her to Ragnor's house, but Ragnor is dead and Magnus is there in his place. Magnus temporarily freezes Sebastian so that he cannot hear and tells Clary to bring him a spell book from the Wayland country home, and she convinces Jace to take her there.


Together, they find Valentine's underground lab, where a dying angel tells them that Jace was imbued with demon blood by Valentine while in the womb. The manor collapses, but Jace and Clary escape by jumping out of the house therefore landing in the grass. They kiss each other but Clary gets frustrated because she feels Jace only wants another reason to loath himself because he believes he has demon blood in him. They return to Alicante in silence only to find the city in flames: the demon wards are down.

Alec, Isabelle, Aline, Sebastian and Max are attacked by demons in Alicante. Luke's pack of werewolves also arrives to help. Alec leaves to fight them while Sebastian, Max and Isabelle hide; however, Max disappears, and Sebastian attacks Isabelle. Jace and Clary meet Alec at the Gard. Clary gives the spell book she recovered to Magnus, who promises to cure her mother, then leaves with the other two to break Simon out of jail.

While there, they also release Hodge, who tells them that the final Mortal Instrument—the mirror—is in fact the waters of Lake Lyn. Sebastian arrives, kills Hodge, and admits he is a spy for Valentine. From there, he throws Jace into a tree, hits Clary in the face, breaks Alec's bow, is attacked by Simon, and then runs away. The others learn that he also killed Max.


Valentine gives the Clave until midnight the next day to surrender; if they do not, he will kill every Shadowhunter left. He kills the Inquisitor before leaving. Jace and Clary talk, and Jace tells Clary that he loves her, and they sleep together in a bed (with no intercourse involved). Jace leaves Clary in the morning, leaving Clary a note saying he has gone to find Sebastian. Clary's mother arrives, woken from her coma, and they argue.

Clary storms out, and goes to a hill then Simon finds her there and talks to her then, they see the Clave preparing to surrender. Clary remembers a rune the dying angel showed her, which can be used to bind a Downworlder and a Shadowhunter so that they share each others' powers and she also knows a partner rune. She tells the Clave, and people begin bonding, including Alec and Magnus, who reveal that they have been having a relationship.

Jocelyn tells Clary that Clary was given angel's blood in the womb, hence her power to create new runes, and also that Sebastian, not Jace, is the brother who was given demon blood. Jace is not Clary's brother, but he was also given angel blood, explaining his supernatural jumping ability. Meanwhile, Raphael agrees with the Clave that the vampires will fight if the Clave give them Simon; Simon agrees, but first Clary marks him with the first Mark ever made: the Mark of Cain. Raphael cannot kill Simon as he plans to as it will rebound on him seven-fold, although this means Simon will have to fight.

Jace overhears Valentine and Sebastian talking, and learns that Valentine plans to summon Raziel at Lake Lyn. After Valentine leaves, the two boys fight, and Sebastian tells Jace that he is Clary's brother, not Jace. Sebastian almost kills Jace, but Isabelle arrives to help Jace kill Sebastian, even though his body is never recovered, proving a point that would make you wonder. Also, Isabelle tells Jace he's not Clary's brother.

Clary travels by portal to Lake Lyn to stop Valentine from summoning Raziel but is knocked out on the way. Valentine binds and silences her with runes, then tries to kill her, but Jace arrives and saves her life. Valentine then proceeds to kill Jace and summon Raziel. Raziel, however, sees through Valentine's selfish plans, kills Valentine and instead offers Clary a wish.

The runes now gone, she asks the angel for Jace to be alive again. He grants it and they are rescued by Shadowhunters going to the lake. Jace and Clary express their feelings to one another and make it publicly known by walking into a crowd holding hands. The book ends with all of the remaining main and recurring characters sitting in Alicante watching a fireworks show, which Clary thinks look like falling angels.