The story begins with Clary Fray, she is a totally normal girl who lives an ordinary life. We meet Clary as she is going out with her friend Simon Lewis, they are going to a club called Pandemonium. They arrive at the club and at first its fun. Things take a turn for the worse when during the night Clary sees a man getting killed by a group of tennagers. These teenagers are brutal and they kill the man without mercy. The strange thing is, nobody but Clary can see these teenagers. They commited the murder right in the middle of the dance floor but nobody notices. Clary is so scared that she screams. The group of teenagers notices this and they run away. One of the killers notices Clary and he seems to be familiar with her.
The following day Clary wakes up and she wants to forget about what happened last night. That might prove to be a bit more difficult than she imagined because it seems that in her sleep she has drawn many strange symbols all over her room. Clary is now more scared than ever and decides that she has to get out of the house. She goes to get some coffee at a local coffee shop and there she wants to meet up with Simon. When they meet up Simon is really worried about Clary. He thinks that she is losing her sanity and has become unstable as her story makes no sense. Clary notices that the man from the night before is nearby and is watching her. Clary wants to know what is going on so she goes outside and confronts this man about his actions.
Clary then shows the man the symbols that she has drawn during the night and she wants to know why she is the only one who can see him. This man is now very interested in Clary and realizes that she is no ordinary human. This man reveals himself as Jace Wayland and he tells Clary that she is not a mundane. Mundane are ordinary humans without powers, Clary is something far more special. Clary is now more confused than ever and wants answers about her origins. Suddenly Clary gets a very scary phone call from her mother Jocelyn. Clary wants to know what is wrong but her mother tells her that she must not come home. The last message that she gives to her daughter is to contact someone named Luke.
Clary runs back home but when she arrives there her mother is totally gone. Their entire home is totally destroyed. Clary then sees a demon monster called Ravener. Jace also arrives and attacks the demon with fire and uses his special blade to kill it. Jace then reveals to Clary that there is a world of demons all around humanity. Clary soon finds out that her mother was a Shadowhunter and that she also has special powers. While talking to a tarot card reader Jace notices that Clary might be connected to something called the Mortal Cup.
Jace and Clary meet up with Simon. The trio then decides that they will search for Clary’s mother together. Jace also notices that there is a burnt photo of what seems to be Clary’s father. Jace and Clary meet two other Shadowhunters named Pangborn and Blackwell who are interrogating Luke. Luke is being interrogated and he reveals that he does not care about Clary and her mother. Jace starts to fight the two Shadowhunters while Clary runs away.
A demon attacks Simon and Clary must save his life. Jace also arrives and manages to kill the demon. The trio then runs away and they go to an old Gothic cathedral. Simon and other normal humans cannot see this cathedral as its part of the magic. The magic that protects the cathedral is called glamour. When they finally enter the Institute Clary falls down because she was poisoned by the demon. Jace saves her and takes her to the infirmary to heal.
Jace also has two adoptive siblings, one is called Isabelle and the other Alec. Clary gets a new set of clothes and then meets Hodge Starkweather who is the tutor in the Institute. Clary gets introduced to many aspects of the Shadowhunter society and in the meantime Jace sends a secret message to the Silent City and the Silent Brothers. In this message he demands that they search through Clary’s memories so they can find out more about her origins. Clary and Jace then depart to the Silent City and we learn that the city is also called City of Bones. When they arrive they meet Brother Jeremiah and he brings them inside. Soon the Brothers try to search through Clarys mind and realize that her memories are blocked by some sort of spell and they cannot find them. After several more attempts they only unlock some fragments showing Clary drawing the angelic rune. They also find a name from her memories, the name is Magnus Bane. Clary and Jace leave as the Brothers cannot find any more relevant information from her memories. Jace and Clary decide that they must find Magnus Bane.
Clary, Alec, Isabelle, Jace and Simon all join forces and soon they manage to find where Magnus is located. It’s revealed that Magnus is actually a very powerful Warlock who lives in Brooklyn. He was the one who actually put the block on Clary. This was done because her mother demanded that Clary be protected. Jocelyn sent her daughter Clary to Magnus several times over the years so that he could block her memories. Clary’s mother really wanted to give her daughter a totally normal life and to keep her safe from demons. Over the years Magnus realized that Clary’s memories just keep coming back and it is really difficult to block them. Simon drops his guard and drinks a poisoned drink. After he is poisoned Simon also gets kidnapped by a bunch of vampires. The group all try to save Simon as he is taken to a Hotel that is basically now acting as a vampire lair. Clary and the rest of the Shadowhunters all grab special weapons and then they go save Simon. While at first they manage to save Simon, soon they are attacked by many vampires. While they fight with everything they have it seems that the vampires are just more powerful. Suddenly a bunch of werewolves arrive and they start to fight the vampires. Clary fights one of the werewolves and soon the group manages to run away and save Simon. He has to be healed for a longer time as he was badly injured in the fight.
Alec wants Clary to return back to the normal human world as she is putting Jace and the others in danger by being here. Clary soon realizes that Alec is actually in love with Jace and he does not want to reveal his true feelings. Alec then attacks Claire and demands that she keep his secret.
The day of Clary’s birthday has arrived and that same night she and Jace spend some time alone. They have a romantic moment and share a kiss. Later they go back to her room as Simon is looking for Clary everywhere. Simon and Clary talk about the kiss later and Clary tries to defend herself by saying that the kiss did not mean anything. Jace overhears this and is saddened by the fact. Simon and Clary also get into a fight and he finally confesses that he has been in love with her since they were kids.
Clary is overwhelmed and she goes back to her room to draw in her notebook. Clary soon realizes that she knows where the Mortal Cup is actually located and she can find it. Clary tells this information to the rest of the group and all of them go visit Madame Dorothea. When they arrive it’s revealed that a demon has actually possessed the Madam. Alec tries to fight the demon but gets hurt. Simon manages to save the entire group. They actually find the Mortal Cup and bring it back to the Institute. Magnus Bane uses his special powers to save Alec and prevent him from dying.
Clary gives the Mortal Cup to Hodge and it is then revealed that Hodge has been working for a man called Valentine Morgenstern. This man Valentine is a known villain who was thought to be dead for many years. Valentine then appears from a portal and wants Clary to drink blood from the Cup. Clary tricks Valentine and jumps into a portal. Valentine then reveals that he has information that shows Jace and Clary are actually brother and sister.
Clary meets up with Luke outside his shop and he shows his true nature, he is actually a werewolf. Luke reveals that he only wanted to protect Clary and her mother and that he actually wants to always be by their side. Luke decides to help Clary and he summons other werewolves and they all attack the Institute. Valentine then summons many demons. Clary and Isabelle are joined by Luke and his werewolfs and they all start to battle the demons. Clary manages to extract a rune from her hand and she stops the demons. The group escapes the demon attack. Isabelle and Simon try to close the portal that is releasing all the demons. Hodge decides to help them and they finally close the portal. The demons now have no way to enter the human world.
Soon Clary finds Valentine and he reveals that Jace is his son and that he is also her father. Clary and Jace are actually brother and sister. Both of them are now horrified as they realize that they are siblings and also they are in love. Valentine is happy that they are now totally weak and demoralized. Valentine then demands that Claire should consume the blood from the Cup but she still refuses. Valentine is so furious that he starts to hurt her. Jace wants to protect Clary so he starts to fight Valentine with his blades. Valentine is very skilled in his fighting style.
Their fight is brutal and both of them use all of their strength. During the fight they accidentally knock the card and Cup right next to Clary. Clary soon realizes that Jace is losing the fight and she wants to save him. Clary tells Valentine that she will throw the Cup through the portal. Valentine stops himself from killing Jace and then goes for the portal. Clary then reveals that her real father would know her true thoughts and that he is a fraud. Clary gives Valentine a replica of the Cup and throws him into the portal. Clary and Jace think that the battle is finally over but Valentine tries to grab Clary. Jace and Clary join forces and freeze the portal, totally severing Valentine from his hand.
The battle is now finally over. It starts to snow as Jace and Clary are left alone. They both realize that they have a forbidden love that could destroy both of them. After that Clary finds her mother who is now in a coma. She has been poisoned and she has to be put in a hospital. Clary then returns back to her apartment and uses her new powers to create powerful runes. Jace then arrives and invites her to come back to the Institute. Jace tells her that she is very special and they should fight demons together, even if their love is forbidden. He also tells Clary that she is the most courageous mundane he has ever met. Clary decides to officially join the Shadowhunters and train to become a real fighter. Jace and Clary jump on his bike and its a bit awkward at first. They are still not sure if they are actually siblings. Both Jace and Clary think that Valentine lied to them so they drive off and continue their adventures.