Jace Wayland finds himself caught in the lies his father, Valentine, created. The young Shadowhunter, a being created from humans and angels, is under suspicion for being in league with his father to destroy the Clave — the governing body of the Shadowhunters. Even Jace’s adopted mother suspects his motives for remaining in the human world. She questions why Jace didn’t return to the Shadowhunters’ home when his father escaped with the Mortal Cup, a powerful Shadowhunter relic.
Clary Fray, another Shadowhunter, wrestles with her emotions. She and Jace fell in love before discovering they were siblings. Her best friend, Simon, is also in love with her, and she can’t work out her feelings for either boy. In addition, her mother remains in a coma that Clary believes Valentine, her father, caused.
When Jace runs from the Institute, a sanctuary for Shadowhunters, he picks a fight with a werewolf. It is a desperate cry for help, as he knows it will bring Clary’s surrogate father, Luke — also a werewolf — to sort out the damage. Jace asks Luke and Clary to accompany him back to the Institute. They discover that the Clave has sent The Inquisitor to question Jace. The Inquisitor doesn’t appreciate Jace’s arrogance and orders him incarcerated in the Silent City, a prison for Shadowhunters.
That night Valentine attacks the prison, killing all of the Silent Brothers that guard it. He finds Jace and explains that he killed the Brothers in order to steal Maellartach, the sword they were sworn to protect. Clary, along with Jace’s adopted brother and sister, interrupt Valentine before he can defend his actions to Jace.
While Jace recovers from demonic poisoning at the home of Magnus, the High Warlock of Brooklyn, they deduce that Valentine stole Maellartach so he could call demons and force them to do his will. In order to perform the ritual necessary to convert the sword to his control, Valentine needs to dip it in the blood of the four kinds of Downworld children — a warlock, a faerie, a werewolf and a vampire. A warlock and a faerie have already been murdered. When the Queen of the Seelie, or faerie, Court requests an audience with them, the Shadowhunters reluctantly agree. They hope to convince the Queen of Valentine’s plan and enlist her aid in the coming battle against him.
The Queen doesn’t agree to help them, but she does dangle tidbits of information regarding Clary and Jace’s heritage, calling them “Valentine’s experiments.” She suggests that he gave them each a gift. Clary has the gift of words that can’t be spoken, and Jace has the “Angel’s own gift,” but she doesn’t say what that is. Clary is trapped in the Seelie underworld after she accidently licks some faerie juice off her fingers. The Queen agrees to let her leave if Clary receives the kiss she most desires. When Simon’s kiss fails to lift the curse, Jace steps forward. His kiss frees Clary, but not without devastating Simon. Before Clary can talk with him, Simon runs away.
Jace and Clary try and sort out their feelings for each other but are interrupted when they find that vampires have attacked Simon. The vampire leader returns Simon’s body to the Institute so the Shadowhunters can decide what should become of him. Clary has to choose between brutally killing Simon and allowing him to live as a vampire. Unable to bear losing him, she allows him to be turned into a Downworlder.
The Inquisitor imprisons Jace after she discovers he has talked with Valentine. Jace tries to convince her that Valentine is close to having his demon army ready to attack, but the Inquisitor doesn’t believe him. Instead, she tries to use Jace as a bargaining chip. She informs Valentine that she will kill Jace unless he returns the Mortal Instruments, the Mortal Cup and Maellartach to the Clave, but Valentine refuses to submit. Jace discovers his special gift after the Inquisitor leaves him imprisoned in an electrical force field. The only way out is to jump 30 feet in the air to clear the walls. Desperate to defeat his father, Jace summons all his strength and jumps from the cell.
Valentine kidnaps Simon and a female werewolf. He wants to use their blood to complete Maellartach’s transformation. Demons attack the Shadowhunters, and in a final showdown, Clary uses her gift, that of words that can’t be spoken. Clary carves the rune for “open” on the wall of the ship. The boat tears apart and eventually explodes. Valentine escapes with the Mortal Cup and Maellartach, but most of the Shadowhunters survive.
Jace and his adoptive mother make amends. Simon tells Clary that he still wants to be friends. When Clary goes to visit her mother at the hospital, she meets a woman who says she knows how to reverse the spell Clary’s mother is under.