The night of the murder, Clary Fray follows three teenagers with strange tattoos into a storeroom at the Pandemonium Club, expecting to stop a crime. Instead, she watches as a boy with electric-blue hair is struck down by a blade that shines like crystal. Before her eyes, the body vanishes into thin air, leaving not so much as a smear of blood on the dusty floor. The killers are just as puzzled by her as she is by them. They are Shadowhunters, warriors who rid the world of demons, and they are invisible to ordinary humans. “A mundie girl,” says the blond one, Jace, his golden eyes narrowed in disbelief. “And she can see us.”
Clary's ordinary life unravels within twenty-four hours. A frantic, terrified phone call from her mother ends in a crash of splintering wood and a slithering, inhuman sound. “Don't come home!” her mother screams, but Clary runs, finding their apartment ransacked and a grotesque, scorpion-like demon waiting for her. It hisses of a man named Valentine and a desire to eat her flesh. She survives only by instinct, jamming a strange device Jace left behind down the creature's throat. Jace finds her moments later, collapsed in the garden, and as the world dissolves into blackness, he carries her away from the mundane world and into his own.
She awakens three days later in the infirmary of the New York Institute, a cavernous, cathedral-like sanctuary for Shadowhunters. Here, in this world of shadows and secrets, she is an anomaly. She learns of the Clave, the governing body of demon hunters, and of Downworlders - vampires, werewolves, and warlocks who share the city with unsuspecting humans. She learns of the Mortal Cup, a sacred object lost years ago, and of Valentine, a rogue Shadowhunter who led a bloody uprising and was believed to be dead. Jace, with his caustic wit and scarred hands, suspects Clary is not the mundane she believes herself to be; no ordinary human could survive a demon's poison or bear the sight of their world.
Her only link to her old life, her mother's friend Luke, turns her away with cold finality. “I'm not your father, Clary,” he says over the phone. “I've got my own problems.” Alone and adrift, Clary follows Jace back to her ravaged home, where they are attacked by a mindless, rune-scarred creature known as a Forsaken. They learn the truth from the witch downstairs, Madame Dorothea: Clary's mother was a Shadowhunter, living in hiding. And she hid the Mortal Cup itself within a deck of tarot cards she painted, concealing the powerful artifact in plain sight.
An accidental trip through a magical Portal lands Clary and Jace at Luke's bookstore, where they find Clary's best friend, Simon, spying on the man he believes has abandoned them. Hiding, they witness a chilling meeting between Luke and two of Valentine's followers. They speak of Jocelyn being held captive, of the search for the Cup, and of Luke's chilling indifference. “I'm not interested,” he tells them, refusing to help save her. The meeting ends with a final shock, as Jace recognizes the two men. “Those are the men,” he says, his voice hollow, “who murdered my father.”
The search for answers leads them to a party hosted by Magnus Bane, the High Warlock of Brooklyn. Amidst a throng of glittering faeries, sharp-toothed vampires, and nixies with seaweed in their hair, Clary confronts the warlock and learns the devastating truth. For years, her mother brought her to Magnus to have her memories of the Shadow World erased, a spell woven and re-woven to blind her to the truth of her own heritage. “It was the way she wanted it,” Magnus tells her, a desperate attempt to give her a normal, safe life. Before they can learn more, a mis-chosen cocktail transforms Simon into a rat, and he is snatched from Clary's bag by a vampire.
A desperate rescue mission takes Clary and Jace to the Hotel Dumort, a derelict building teeming with the undead. They are ambushed, their plan to trade the vampire leader's life for Simon's going horribly wrong. Just as they are about to be overwhelmed, the hotel's windows explode inward, and a pack of werewolves surges into the room, turning the standoff into a bloody war between vampires and lycanthropes. Jace and Clary escape the carnage on a stolen vampire motorcycle, taking flight over the East River just as the sun begins to rise, the bike's demon energy failing as they crash-land in a Brooklyn parking lot.
Back at the Institute, their brief victory turns to ash. Hodge, their trusted tutor, reveals his allegiance to Valentine. He seizes the Mortal Cup, and in a final act of betrayal, delivers both the Cup and an unconscious Jace to Valentine, who appears through a shimmering Portal. As Valentine vanishes, Luke appears, revealing his own secret: he is a werewolf, and his earlier rejection of Clary was a lie to protect her. He tells her the full, tragic story of her parents: her mother, Jocelyn, was married to Valentine, and they were both members of a radical group called the Circle. Luke, their closest friend, was turned into a werewolf by Valentine's treachery.
The final confrontation takes place in the ruins of an old smallpox hospital. Luke and his wolf pack battle Valentine's Forsaken on the lawn while Clary searches for Jace and her mother. She finds Jace, not a prisoner, but standing beside the man he has just been told is his long-lost father, Michael Wayland, returned from the dead. But it is another lie. As Luke bursts in, the truth is finally laid bare. “This is my father,” Jace says, indicating Valentine, who smiles coolly. “And Clary - Clary is your sister.”
In the devastating aftermath, Jace is forced to choose between the father he just found and the girl he is beginning to love. He chooses Clary, turning on Valentine, but the man escapes through a mirror Portal, taking the Mortal Cup with him and shattering the gateway behind him. Jace is left broken, his world destroyed. In the quiet of the Institute's greenhouse, beneath a sky full of stars, he and Clary are left with the impossible truth of who they are to each other. Days later, they fly over the glittering, magic-filled city on a stolen motorcycle, two siblings bound by blood and tragedy, the ascent beckoning them toward an unknown future.
