Clary goes to the Pandemonium club with her best friend, Simon Lewis, and sees a blue-haired boy sneak into a storeroom with a girl, pursued by two other boys, one armed with what appears to be a knife. Clary sends Simon for help and follows the group. At the storeroom, she witnesses the boy being killed, before vanishing. Simon later appears with a bouncer and asks why Clary is there alone; she realizes no one else can see the others.
The next day, Jocelyn (Clary’s mother) announces they are moving from New York to the country for the summer, where her friend, Luke, has a house. Clary, who knows almost nothing about her mother or her family, is upset by the decision. Simon mentions seeing thin, white scars on Jocelyn's back and shoulders, but Clary dismisses this. The two friends go to a poetry reading where Clary sees Jace, one of the boys from the previous night, who privately tells her about demon-hunters, called Shadowhunters or Nephilim. Jace claims Clary is not a 'mundane', a term for ordinary humans, as she has the Sight, allowing her to see beings from the Shadow World. Clary answers a call from Jocelyn, who frantically warns her not to come home and to tell Luke that "he" has found her. It ends abruptly.
Clary returns to her house, which is in disarray, and finds her mother gone. She is attacked by a demon, which she kills with Jace's Sensor (a device used by Shadowhunters to detect demon energy). Jace brings Clary to the "Institute": the local headquarters of the Shadowhunters, where she is introduced to Isabelle, Alec, and their tutor, Hodge. Jace proves that Clary has Nephilim blood by touching her with a stele, which leaves her unharmed. All Nephilim are unharmed by steles, weapons used to mark Shadowhunters with angelic runes that give them their powers.
Returning to the house, Jace and Clary meet neighbour Madame Dorothea, who has a teleportation portal. To find her mother, Clary, followed by Jace, rushes through the portal. They land at Luke's bookstore and find Simon, in search of Clary. The three hide. Luke returns with two men, Pangborn and Blackwell, whom Valentine sent to interrogate Luke about the Mortal Cup: a talisman sought by both parties. Luke claims ignorance of where Jocelyn hid the Cup and refuses to negotiate with them or interfere with Valentine's plans.
Clary, Jace and Simon then talk to Hodge, who tells them about the Circle: a group of Shadowhunters that Valentine formed to eliminate all Downworlders (vampires, werewolves, faeries, warlocks, and others), which Jocelyn, Valentine's wife, joined when she was younger. Clary is actually Valentine's daughter. Alongside Jocelyn, Alec and Isabelle's parents also used to be Circle Members; Luke was also a member and was a Shadowhunter and the parabatai - one half of a sacred bond between Shadowhunters - of Valentine.
Clary and Jace go to the Silent City to speak to the Silent Brothers, who tell them that a block in her mind prevents her from remembering the Shadow World; placed by warlock Magnus Bane.
At a party hosted by Magnus, Clary meets him. He says his spell is too complex to remove but will fade naturally and was placed at the behest of Jocelyn for Clary's protection. During the party, Simon ignores Isabelle's warning and drinks a blue liquid that transforms him into a rat. Vampires take him away thinking Simon was one of their own, but Clary and Jace rescue him and restore him to human form. That night, Jace takes Clary to the Institute's greenhouse on a midnight picnic to celebrate Clary's sixteenth birthday, where he kisses her. When Simon walks in on them, she pulls away. Hurt, Jace acts coldly towards her.
As her memories emerge, Clary deduces that the Cup is hidden in one of Madame Dorothea's tarot cards. Clary retrieves the Cup, but the demon Abaddon, who has possessed Madame Dorothea and is disguised as her, attempts to take it. Aided by Simon, she escapes and returns to the Institute where Hodge hands over the Cup and an unconscious Jace to Valentine. Hodge flees, pursued by Clary. Hodge attacks her in an alleyway, but she is saved by Luke, who is a werewolf. While Luke's werewolf pack attacks Valentine's followers at Renwick's, Clary locates her unconscious mother and finds Jace. Valentine identifies him as his son; dismaying both Jace and Clary, who were attempting to enter into a romantic relationship. Valentine entices Jace to return to Idris - their home country - with him. Jace refuses, and Valentine escapes through a portal with the Cup, smashing it behind him.
Jace and Clary are honored for their adventure and Alec recovers with the help of Magnus Bane.
