Clary Fray, a fifteen year old girl caught between the world of the supernatural and mortals finds herself dealing with her best friend Simon's transformation into a vampire and her boyfriend withdrawing from her as he fears he will kill her. Clary Fray wanted nothing more than to be your normal high school student, unfortunately the day she meant Jace Wayland, that all changed when she discovered she was one of the last Shadow Hunters (slayers of all the dark things in the world and what goes bump in the night). While she is trying hard to keep some fragment of her normal life, it seems that the supernatural world refuses to let go of her. Especially now, when her best friend and ex-boyfriend Simon is now going through major changes of his own as he transitions into a vampire. Simon is forced with a decision as he goes through these changes, join the new leader Camille who promises him a place within the society of the Daylighters (Vampires who can walk in the sun) or follow the original leader of the vampire's Raphael.
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While he can't decide yet, Simon is also dealing with his mother at home who is growing more suspicious by the day as she wonders why he is never home and constantly looking sickly. As he tries to thwart her questions and increasing worry, Simon is also finding himself under attack by various beings who are after him. During one such attack his mother witnesses, he is able to use his new power of mind control to convince her what she saw was a dream. Realizing it is too dangerous to live in his home any longer, Simon moves in his a member of his band Kyle, however he has not escaped the supernatural realm yet as he catches Kyle changing into a werewolf during the full moon. Realizing his friend has been keeping a dark secret from him, Simon decides to confide in Kyle who more than understands and promises to help him in any way he can.
Clary on the other hand is dealing with Jace, her boyfriend and fellow Shadow Hunter, not wanting to be around her since he is having dreams of killing her. Clary's mother is also struggling with their relationship due to the fact it reminds her of her own with Clary's father, Valentine who turned to evil rather than light and tried to kill Clary months before. This puts a damper on the whole situation which is bringing Clary to a point of wishing she could go back to the way things were before. Clary realizes life as a Shadow Hunter has its ups and downs but wishes she could be with Jace without the supernatural interruptions. She can't help but be worried about Simon and the fact they dated briefly is only creating more problems and causing Jace to withdraw even further.
Meanwhile, Simon falls ill during one of his band's performances and attacks a young girl named Maureen who is the only fan the band has. After the attack, Simon is confronted by his two girlfriend's Maia and Isabelle since they figured out he is dating both of them at the same time. Furious they tell him he has to choose but before he can he receives word that someone dear to him has been kidnapped. Realizing it is Maureen, he follows the instructions of the ransom note. Simon arrives at an abandoned warehouse and can immediately sense there is a problem. As he moves through the dark rooms he discovers the body of Maureen dead and completely drained of blood. Simon is wracked with guilt and wishes he had never let Maureen become their groupie in the first place.
Later in the week, Clary goes to a church where she believes a book can be found that can create Forsaken children (babies who have been infused with darkness), however while there she is attacked by a mythical creature known as a hydra. She thankfully is able to slay the beast but is gravely injured and is rescued by Simon's girlfriend and Shadow Hunter, Isabelle. Clary returns with Isabelle to the Institute ( a place where Shadow Hunters are trained). Isabelle informs Jace of the attack and he rushes to see Clary and they kiss. He apologizes for remaining distant and asks her forgiveness. She of course gives it and they proclaim their love once again. Clary tries to take their relationship to the next level but Jace is reluctant and admits that he is continuing to have the nightmares about hurting her. Worrying this could have an even more negative effect on their relationship, Clary tells Jace she will help him with his issues and takes him to the Silent Brothers in the Silent City (wise men who can see into the future).
The Silent Brothers conclude Jace has been having trouble due to his resurrection by the angel Raziel after he was killed by Valentine months prior. Since all Shadow Hunters receive a spell of protection when they are born, due to him going through a death and rebirth he is without any protection from the darkness. The Silent Brothers reveal they can perform the ritual again but will need to do it in the morning. Jace agrees and submits himself to imprisonment. That night, Jace has another dream of hurting Clary. In his dream, his good friend Max appears, telling him he must cut away the bad within him. Unfortunately, Jace has no idea that it is the Forsaken known as Lillith who is controlling the dream. She forces Jace to carve a rune into his flesh that gives her complete control of him.
The next day at Clary's mother's engagement party, Clary is kidnapped by the now possessed Jace. He uses a binding spell to connect them together and flees with her after she loses consciousness. Later, Simon is approached by Maureen who wasn't dead and is now a vampire. She brings Simon to Lillith who demands he brings back Sebastian, a Shadow Hunter that Jace killed months prior. When Simon refuses, Lillith summons Jace and demands he kill Clary if Simon does bring back Sebastian. Simon complies and drains Sebastian's body of blood though there is no assurance it will work. Clary hugs onto Jace and is able to cut the rune that is forcing him to be possessed by Lillith. As he comes back to himself he begs Clary to run but she refuses.
Lillith takes this as her chance and begins to torture Clary but Simon intervenes and kills her. The Clave arrives (Council for the Shadow Hunters) to assess the situation and Jace and Clary steal a moment alone. While on the roof, Jace apologizes for all he has done to her and Clary tells him that she loves him and when you love someone you accept the good and the bad. As they kiss, Jace begins to hear Sebastian's voice in his head, with a warning that he is coming and to be prepared. Realizing that Clary will be in danger as long as Sebastian is alive, he promises to right the sins of his past and keep her safe at all costs.
Best part of story, including ending:
I really enjoyed that Simon was given more book time this novel and we got to see more of the world from his perspective
Best scene in story:
I loved when Simon was forced to resurrect the dark Shadow Hunter Sebastian and bring him back even though Sebastian caused them so much trouble before. You can tell Simon is so conflicted as he wishes for Clary to remain safe yet knows this could bring about so much more trouble than it is worth.
Opinion about the main character:
Clary is beginning to turn into a lovesick puppy that constantly throws others in harm's way in an attempt to have her own happiness. She continues to make stupid decisions and wishes only to be with Jace while her friends and family continue to bite the dust.