When Clary Frey goes to club Pandemonium in New York a blue haired boy catches her eye and she couldn’t help but watch his every move. When his move led him into a storage room with a tall thin dark haired girl, he wasn’t the only boy entering that room. The sight of the two teenagers following the blue haired boy wasn’t as unusual as the sight of the knife in one of their hands. Clary’s best friend Simon went to get help and Clary herself swallowed her panic and went after the teenagers in the storage room. What happened next not only shocked her but the shadowhunters as well. The shadowhunters included Isabelle, the tall thin dark-haired girl, Jace with the knife, and Isabelle’s brother Alec. Just as Clary expected the blue haired boy was in danger. He had been tied up and about to be killed when Clary stepped into the room. Confusion spread through the teenagers however, it didn’t keep the shadowhunters from doing their job. The blue haired boy was a shape shifting demon and had to be sent back to his own dimension. When the body of the boy/demon disappeared Clary realized that strange things were taking place and she could not make sense of them. Then enters Simon with the club’s bouncer behind him, the new comers to the storage room could not see any one but Clary and she had to leave quietly despite her many questions in order to keep a sane persona.
The next day more surprises are thrown at Clary and she barely survives them. Just as any normal teenager, Clary has a fight with her mother over leaving the city for the summer and she runs off with Simon. Despite her better judgment she goes to watch one of Simon’s friends slam some horrible poetry. While at Java Jones, Jace suddenly appears to take Clary back to the institute. Before Clary has a chance to think about what Jace was saying her mother called. Jocelyn Fray was in a frantic state on the other end of the phone line, and told Clary not to come home right before the phone disconnected. Clary was now frantic herself she drops her phone on the concrete and the phone brakes. Clary grabs a phone from Jace and runs toward her apartment only to find out that what she took from Jace wasn’t a phone. When Clary reaches the apartment she discovers it in a mess. Coach cushions ripped and puking cotton innards, Jocelyn’s paintings ripped apart and glass from the frames shattered everywhere. This wasn’t some normal robbery, someone was looking for something. Despite the mess everything seemed to be there except her mother. Jocelyn was gone but a ravener demon was there and by the sound it made it was hungry and Clary just happened to be on the menu. When the demon went for a bite, Clary shoved the devise she had taken from Jace in the half alligator half centipede looking beast’s teeth and it started to shake. The demon was going to disappear back to its own dimension but before leaving it got Clary in the back of her neck and she blacked out.
Clary woke moments later behind the rose bushes her mother tended. Jace was trying to get her back to the institution so Hodge could fix her up but the demon police force in charge of cleaning up demonic caused messes showed up. Jace acted on instinct to hide Clary by way of marking her with a ruin. A ruin could kill any normal Mundane but Clary wasn’t normal. Jace wasn’t convinced that she was a Mundie at all. Clary woke in the institute’s infirmary three days later.
When Clary was able to use the phone and get ahold of Luke, her mother’s best friend and the only father figure Clary has ever known, she was disappointed when he told her to leave him alone and to stay where she was. The institute with the Shadowhunters and their life she knew nothing about. Clary however, needed to go back to her apartment to retrieve some of her things. When Clary and Jace entered the apartment it was empty, nothing but a forsaken—there to attack them—was left.
After Jace defeated the forsaken soldier he hadn’t had enough. Jace was headed back up the stairs to the apartment when Clary’s neighbor Madame Dorothea stopped him. Clary and Jace was intrigued by what Dorothea—mundane raised by a witch—had to say. However, when Jace spotted a five dimensional door in Dorothea’s apartment, Clary goes flying through the portal to Luke’s house with Jace on her heels.
The two shadowhunters ran into the very normal mundane Simon, and Clary told him everything that had happened to her since their departure. She even told him what she knew of the shadow world. When Luke came home the three teenagers hid and were able to find out some interesting facts about Jacelyn and Luke. One fact that they learned was that Valentine and Jocelyn was married.
There was still confusion and things not adding up to much, but one thing that was for certain was that Clary had a block in her mind. After a bone chilling trip to the Bone City seeking help from the silent brothers, Clary learned the name of the person responsible for the spell that blocked her memories. Magnus Bane.
That night Clary, Jace, Isabelle, Alec, and Simon went to a party that the High Warlock of Brooklyn Magnus Bane was hosting. Isabelle just so happened to have an invitation with her. Magnus explained to Clary that he put a spell on her memories by the request of her mother. The spell however could not be undone. Clary would have to wait for the spell to wear off. On the way out Isabelle announced that Simon had turned into a rat by drinking one of the fairy drinks. That spell too would have to just wear off but, before the shadowhunters could leave the party safely one of the vampires stole rat-Simon out of Clary’s bag. Clary and Jace was now in search for the vampire’s lair. With the information Magnus had given them they set off for the Hotel Dumont.
While in the hotel, Clary and Jace found Simon as well as themselves surrounded by vampires. Clary thought things looked bad but, when the wolves crashed in wanting Clary for themselves, the shadowhunters found themselves in the middle of a downworlder war. Clary, Jace, and rat-Simon ran for their lives up to the roof of the hotel and flew off with a flying motorcycle that runs on demon energies.
For Clary’s birthday Jace took her on a picnic up in the greenhouse of the institute. The sweet gestures soon had Jace and Clary kissing but when Simon saw he ruined the mood with his love confession and stomped home.
Later while Clary was messing with her sketch pad she discovered that through a rune she could hide objects in the drawings. Clary realized that’s how her mother hid the mortal cup and she knew exactly where too. In the tarot cards that Jocelyn painted for Dorothea. When Simon drove the shadowhunters over to Dorothea’s apartment no one was surprised when Clary pulled the cup out of the card however, when the Greater Demon came through the portal, all but Dorothea was shocked. When the shadowhunters were being crushed by the demon Abbadon, Simon busted in and saved the day with his excellent archery skills.
Back at the institute Hodge learned of their success with retrieving the mortal cup and attacked Clary and Jace in order to hand the cup over to Valentine. When Valentine came, he lifted the curse that bound Hodge to the institute and took the mortal cup as well as Jace with him through the portal he had arrived from.
Clary was trapped in an invisible cage but when she realized she still had Jace’s Steele she used it to shatter the invisible wall around her. Now nothing was in her way to go after Hodge for what he had done. When she found him he wasn’t going to give up without a fight. When Hodge was about to slice Clary up with his chakram a wolf jumped in and attacked him. When the wolf turned on Clary she knocked her head hard enough to black out.
When Clary woke she was in a jail cell and when Luke walked in he told her everything about him being the wolf and about her mom and Valentine and how Valentine is her dad. Clary knew that Valentine had used a portal to enter the institution so he must have been hiding some place near a portal. Magnus had said there were only two portals in New York; one at Dorothea’s which was destroyed when the Greater Demon came through it and, the other at Renwick’s. Clary found with the help of Simon that Renwick’s was a hospital for small pox located on the south end of Roosevelt Island.
Luke gathered on army of lycanthropes and together they headed for Renwick’s to retrieve Jocelyn, Jace, and the mortal cup from Valentine. Clary and Luke found Jocelyn still asleep under a spell and chained to a bed. Luke fought off Valentine’s men while Clary ran in search for Jace. She found Jace but was not expecting to see him in such good shape. Jace explained to Clary that his father wasn’t dead and when Valentine walked in he explained to Clary how he was Jace’s father as well as hers. Clary and Jace were taking two different sides when it came to the matter of Valentine. When Luke was about to die at the hand of Valentine though, Jace stepped in to stop him. Jace was going to kill Valentine himself but could not bring himself to do it so Valentine escaped through the portal smashing it in his wake.