The third book in the Mortal Instruments series starts a week after City of Ashes. The Lightwoods, Jace, and Clary are leaving for the city of Alicante that evening with the help of Magnus who was going to open a Portal. However, Simon goes to the Institute, where he and the Shadowhunters (except Clary) are attacked by dozens of Forsaken. One of them ends up hurting Simon. Magnus Bane opens the Portal they were using to get to Alicante that night, and the group jumps through to escape their attackers, taking Simon with them. Clary finds out and is infuriated because they left her, and in her anger creates a Portal to the city. Luke, knowing she could hurt herself, jumps in with her. They land in Lake Lyn, where the angel Raziel came out of to make the first Shadowhunters. Clary swallows some of the water and, because of the lake’s cursed magical properties, she begins to fever and hallucinate while she and Luke walk to Alicante. Luke gets Clary help from his sister, Amatis Herondale, (Stephen Herondale's first wife). Amatis agrees to let Clary stay with her.
Meanwhile, Jace, Simon, and the Lightwoods are introduced to Aline Penhallow, and her handsome cousin Sebastian Verlac. Jace immediately dislikes Sebastian, and flirts with Aline - a fact that angers Simon. Alec is ordered to bring Simon to meet the new Inquisitor, who is curious as to why they brought a Downworlder into Alicante. Simon, while under the impression that the Clave will Portal him back to New York, is thrown in jail after being interrogated. The next day the Inquisitor talks to him and tells him he wants Simon to lie about the Lightwoods, meaning that they never left Valentine and that they (including Alec, but not Isabelle and Max) are working for him, which Simon refuses and she puts him in jail again.
Clary sneaks out of Amatis’s house to visit the Lightwoods, where she catches Jace and Aline kissing and has a big argument with Jace. Leaving in anger, she runs into Sebastian, and tells him about how her mother is in a magical coma, and that she needs to find the warlock Ragnor Fell to fix it. Jace lashes out at Alec, admits that he knows Alec thinks himself to be in love with him but says that it is because he (Jace) was “safe”, and an excuse to not get into a relationship with Magnus.
Clary and Sebastian go to Ragnor’s house the next day, and Clary (while Sebastian is frozen because Magnus doesn’t trust him) is shocked to learn that Ragnor was killed and Magnus was there in his place. Magnus tells Clary what she needs, and the answer is in a spell book disguised as a cookbook in the Wayland country home. Sebastian takes Clary to the ruins of Fairchild manor where he kisses her but she pushes him away. Sebastian then tells Clary about Simon being in jail. In jail Raphael (in projection=not corporally there) visits Simon and tells him to go far where no one can find him because he (Simon) is dangerous for the vampire species...