In the beginning of City of Bones, Clary is unaware that she is a shadowhunter. Alongside her best friend Simon, who secretly has feelings for her, they go to a night club. It is at this place where Clary encounters Jace, Alec, and Isabella and witnesses Jace killing a boy, whom he claims to be a demon. The next day, Clary receives an alarming phone call from her mother telling her not to come back home. Rushing back home, Clary finds her mother missing, her apartment in chaos, and a demon waiting for her.
Clary successfully kills a demon, but sustains injuries in the process. Jace discovers her and takes her to the Institute, where he resides and learns about being a shadowhunter. After awakening from a coma caused by demon blood poisoning, Clary officially meets Alec, Isabella L
...ightwood, and Hodge, the children's tutor. They are puzzled by Clary's sudden ability to see them, which they refer to as the Sight. To investigate this phenomenon, they call upon a Silent Brother, who is a member of a group of men known for their inability to speak. Notably, the Silent Brothers possess the unique ability to enter people's minds and observe their memories.
They communicate telepathically as well. If Brother Jeremiah cannot access Clary's memories, she must accompany Jace to the Silent City, where all the Brothers collaborate on her case. Within the Silent City, the brothers collectively delve into her mind, but encounter a barrier that obstructs her recollections and past experiences. The only piece of information they have is a name: Magnus Bane. During their visit to Magnus Bane's party in
Brooklyn, Clary learns more about the memory blockage imposed on her by Magnus, who happens to be a warlock.
Clary's mother prevented him from having any connection with the shadowhunting world. During the party, Simon unknowingly transforms into a rat after consuming a faerie beverage. When he is mistakenly captured by a vampire, Clary and Jace venture to Hotel Dumort in search of Simon. They engage in a confrontation with the vampires, resulting in Simon biting their temporary leader, Raphael. Subsequently, Simon discovers that he has been transformed into a vampire. Later in the evening, while on the rooftop, Clary and Jace share a kiss.
Clary still has to locate her mother and retrieve the mortal cup before it falls into the hands of Valentine, a shadowhunter who previously attempted to lead a rebellion against the clave. Along her journey, Clary discovers her unique talent - the ability to create new runes that are not documented in the grey book. To her surprise, she uncovers the mortal cup hidden within a deck of playing cards crafted by her mother for their neighbor. Astonishingly, Valentine is revealed to be both Jace and Clary's father. As Hodge betrays them by surrendering the mortal cup to Valentine in exchange for the removal of his curse, Valentine seizes the opportunity to take Jace with him as well.
Clary and Luke, who is a werewolf and her mother's friend, team up to chase Valentine in search of Jace and Clary's mother. Upon arriving at Valentine's hideout, they encounter a group of Forsaken. While Luke's pack fights the Forsaken, Clary and Luke enter the building. Within, they discover
Clary's mother in a self-induced coma, as well as Valentine and Jace. Despite having the opportunity to kill Valentine, Jace cannot bring himself to do so due to Valentine raising him. In the end, Valentine manages to escape to Idris with the mortal cup.
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