Fifteen year-old Clary Fray’s life is turned upside down when she tries to stop what she thinks is a random knife attack at an underage dance club. The knife-wielding punks she follows into a storage room are actually Nephilim, creatures that are half angel and half human, and the boy they attack is a demon. Clary is stunned when she witnesses the Nephilim, or Shadowhunters, as they prefer to be called, destroy the demon.
Clary’s life is further complicated when her mother disappears after a frantic phone call to Clary. When Clary and Jace, a confident and handsome young Shadowhunter, return to Clary’s apartment, they find it torn apart. The two are attacked by another demon, which Clary ends up killing, but not before it poisons her.
Jace takes Clary to the Institute, a kind of embassy for Shadowhunters, where she can heal. When Clary’s surrogate father, Luke, refuses to let her stay at his home, she is forced to live at the Institute with Jace and his fellow Shadowhunters — Alec, Isabelle and their tutor, Hodge. Clary and Jace are attracted to each other.
Clary discovers that she is a Shadowhunter herself, the daughter of Valentine, one of the most feared and evil of the Nephilim. He wanted to use a relic called the Mortal Cup as a tool to create an army of Nephilim. His goal was to annihilate the Downworlders — vampires, werewolves, witches, fairies and sprites. Downworlders themselves are not demons, but some of their actions lead to evil. She learns that her mother fled Idris, the magical home of the Shadowhunters, before Clary was born in order to hide the Mortal Cup. The Nephilim now believe Valentine, who had been presumed dead, has returned to find the magical chalice.
Clary and the other Shadowhunters find the Mortal Cup. Before it can be placed in safe hands, Valentine steals it. He escapes with the cup and Jace through a portal to an unknown location, which disappears before Clary can follow.
With the help of Luke, who turns out to be a werewolf, and Simon, her best friend before her Shadowhunter realizations, Clary locates where Valentine has hidden her mother, Jace and the Mortal Cup. A battle ensues between the werewolves and Valentine’s minions. Clary finds her mother in a trance and chained to a bed. Unable to rouse her, Clary searches for Jace. When she locates him, she tries to convince him to escape with her, but Jace refuses. Valentine is the father Jace believed had been murdered long ago. Valentine has convinced Jace that he [his father] has fought against a corrupt government in Idris and that all the evil stories about him are false. Jace and Clary realize they are brother and sister.
Luke confronts Valentine. Clary begs Jace to stop Valentine from killing Luke, the only father figure she has ever known. When Jace defends the werewolf, Valentine returns to Idris with the Mortal Cup, leaving Jace alone and fatherless once again.
Clary and Luke take her mother to a hospital where she is attended by not only human doctors but also magical ones in disguise. No one can wake her mother from her trance. Jace and Clary are left to sort out their conflicted emotions now that they believe they are siblings.