New York City teenager Clary Fray begins seeing and drawing a strange symbol, worrying her mother Jocelyn Fray and family friend, Luke Garroway. At a crowded nightclub with her friend, Simon Lewis, Clary is the only one who can see Jace Wayland and his accomplices killing a man. The next day, two men, Emil Pangborn and Samuel Blackwell, arrive at the Fray apartment searching for a cup. Jocelyn calls Clary, frantically telling her to stay away and to warn Luke about someone named Valentine; she then drinks a potion putting her in a deep sleep. Returning home, Clary finds her mother missing and is attacked by a dog-like creature. Jace, a "Shadowhunter", appears and kills it, explaining that it, like the "man" killed at the nightclub, was a demon in another form. With help from the Frays' neighbor, Madame Dorothea, a witch, Jace deduces that Pangborn and Blackwell seek a lost artifact called the Mortal Cup. Jace and Clary, along with Simon, go to Luke's antique store. Pangborn and Blackwell are forcibly interrogating Luke who, to protect Clary and Jocelyn, falsely claims he cares nothing about the Frays and only wants the Mortal Cup. The trio escapes to the Shadowhunter Institute, a hidden cathedral-like building, where Jace treats Clary, who was stung by the demon. She and Simon meet two other Shadowhunters, siblings Alec and Isabelle Lightwood, and Shadowhunter leader, Hodge. Clary learns that Shadowhunters, invisible to mortals, are half-human, half-angel demon slayers. Clary has inherited her Shadowhunter mother's powers, including drawing temporary magical runes on the skin. The Mortal Cup is one of three Mortal Instruments given to the first Shadowhunter by the Angel Raziel. Shadowhunters are either descended from other Shadowhunters or made by drinking from the cup. Hodge explains that Valentine Morgenstern, an ex-Shadowhunter who betrayed the order, now seeks the Cup to control both Shadowhunters and demons. Hodge instructs Jace to take Clary to the City of Bones, a sanctuary beneath a cemetery. When the Silent Brothers attempt to unlock Clary's blocked memories, they uncover a connection to Magnus Bane, the High Warlock of Brooklyn. At Bane's club, he tells Clary that Jocelyn had him block knowledge of the Shadowhunter world from Clary's mind. When Vampires kidnap Simon, Jace, Alec, Isabelle, and Clary trail them to their hideout. They find Simon, but vampires outnumber them. Werewolves intervene and save them.