When Clary Fray witnesses three tattoo-covered teenagers murder another teen, she is unable to prove the crime because the victim disappears right in front of her eyes, and no one else can see the killers.
She learns that the teens are Shadowhunters (humans who hunt and kill demons), and Clary, a mundie (i.e., mundane human), should not be able to see them either. Shortly after this discovery, her mother, Jocelyn, an erstwhile Shadowhunter, is kidnapped.
Jocelyn is the only person who knows the whereabouts of The Mortal Cup, a dangerous magical item that turns humans into Shadowhunters.
Clary must find the cup and keep it from a renegade sector of Shadowhunters bent on eliminating all nonhumans, including benevolent werewolves and friendly vampires.