Fifteen-year-old Clary Fray is partying hard at the Pandemonium Club with her best friend, Simon. There, she sees a crowd of strangely behaving, but incredibly attractive teens sneak into a storeroom. She follows them, and discovers that they're demon hunters when they kill a demon in front of her, which dissolves into the floor. Yuck.
Back at home, her mother is acting all cryptic and over-protective, packing up their stuff to move away from New York City and into the country home of her best friend, Luke. Clary isn't pleased, and leaves the apartment to hang out with Simon. She finds him at a poetry reading, where she also runs into Jace, one of the demon hunters (called Shadowhunters or Nephilim). And then she receives a scary phone call from her mother that sounds like she's being attacked.
Back at the apartment, Clary finds the place deserted. Except, that is, for the giant, slobbering, poisonous demon that bites her. She kills the demon by herself, but not before she's bitten and passes out. Poisoned, Clary is carried to the Institute by Jace, who introduces her to a few other Shadowhunters.
Worried about her missing mother, Clary takes Jace back to her apartment to investigate. They're attacked—again. They seek cover in the apartment of Madame Dorothea, a hacky looking psychic who has ties to the Nephilim. She also has a magical Portal, and Clary, thinking her mother might be through there, rushes through it.
Clary seems to have adopted some sort of act first, ask questions later strategy, which—trust Shmoop—is a bad one. She ends up at her mother's friend Luke's bookstore, where Simon has been lurking, trying to figure out what Luke is up to. She heads back to the Institute, where she finds out more secrets, like the fact that she has a mental block that's preventing her from seeing everything in the Shadowhunter world.
So what's a girl to do? Party, of course. They suit up sexily for a wild party at the apartment of Magnus Bane, the High Warlock of Brooklyn. He's the one who put the block on Clary's memory in the first place, and she totally wants it removed, so crashing the shindig seems like her best bet.
The party's fun enough, except for the fact that Magnus can't remove Clary's mind block. Oh, and Simon gets turned into a rat. He's cute, sure. But he's a rat. Clary puts him into her backpack, but some vindictive vampires steal him and take him to their lair. So Jace and Clary set off to rescue the poor sucker.
Which they do. And then they head back to the Institute again. Jace and Simon have to rest in the infirmary to heal up after a kerfluffle at the vampire lair. That night, Jace takes Clary on a midnight picnic, and their romance blossoms in the greenhouse with a romantic first kiss.
Later, Clary has a light bulb moment. She realizes that her mother must have hidden the Mortal Cup, a magical artifact that is pretty much the most important thing ever, inside a painting—the hand-painted Tarot deck she made for Madame Dorothea.
So it's back to the apartment!
Clary cleverly retrieves the cup, but then an evil demon, Abbadon, rushes through the Portal, possesses Madame Dorothea, and tries to kill Clary and Co. They manage to escape and return to the Institute, where Hodge, Jace's tutor, betrays them by handing over the Cup and an unconscious Jace to Valentine, the Big Bad, whom he had been working with all along.
Gasp! Hodge flees, pursued by Clary. They confront each other in an alleyway, and Hodge attacks her. She's saved by Luke, who is a werewolf. Double gasp!
Luke and Clary formulate a plan to storm Valentine's stronghold. Inside Valentine's castle, which is under a spell that makes it look like a crumbling mental hospital, Clary finds her mother, who is unconscious and chained up.
Then Jace shows up and tells Clary that Valentine is his father. Triple gasp! Which means that Clary and Jace are brother and sister. Okay, we're hyperventilating now. Clary manages to convince Jace that even though Valentine is his father, he's still a murderous, lying buttface. Valentine escapes through a Portal with the Cup, smashing the Portal behind him.
Jace and Clary's story ends with them trying to come to terms with the fact that they're related (and trying to cut back on the flirting). They take one last amazing flying bike ride over the city at night, and Clary appreciates the wonders of the world laid out before her.