After Clary Fray (Lily Collins), a seemingly ordinary teenager, witnesses a murder at a club, she finds out that her mother, Jocelyn (Lena Headey), is attacked in their home in New York City and kidnapped by a man named Valentine (Rhys Meyers) in his search of the Mortal Cup. She calls on a Shadowhunter named Jace (Campbell Bower) and his fellow Shadowhunters, Alec and Isabelle Lightwood (Kevin Zegers and Jemima West), to help her on her quest to rescue her mother and along the way finds out truths about her past and bloodline and becomes the person her mother feared she would become.
Clary learns that Shadowhunters are half-angel (known as "Nephilim") warriors and that she too has the powers of one and tries to harness her powers in time to save her mother. Using her new found gifts, Clary finds the Cup that her mother safely hid, only to be betrayed and forced to relinquish it. Still reeling from this setback and racing to save her mother before it’s too late, Clary finds herself caught in a battle between forces she barely understands