Clary heads to the City of Bones to search for Jace since being captured. She offers to help him, but he begs her to stay away from him.
Alec is feeling better after his recent accident. He asks Magnus out on their first official date as a couple.
The Clave is reassigning Jocelyn to Idris. They're testing her loyalty since she is Valentine's ex-wife. She asks Clary to come with her to Idris so that they can be together and to show her the ways of being a Shadowhunter.
Alec and Isabelle bring Clary to a crime scene. Alec gives Clary a new rune to detect a demon's heat signature and route.
Aldertree sets up a meeting with Raphael. He demands proof Camille is the one causing the crimes and murders or else the blame will fall on their group. Aldertree traps Raphael to a chair and begins torturing him with lasers to find out the truth.
Simon's mother invites him to a family dinner with his sister. He's hesitant but agrees.
Jace has a nightmare about Clary. His cell is next to Hodge and he is warned to not fall asleep in the City of Bones as the guards mess with their minds.
Clary and Alec follow the trail to a frightened girl covered in blood. She was possessed by a demon and isn't sure what happened to her.
Luke begs Jocelyn to stay. He offers to go with her to Idris as he loves her; the two kiss.
Raphael goes to Magnus after the torture. He's covered in scars and needs help.
Isabelle brings the crime scene body back to the Institute. Lydia doesn't have any new information about Jace or his trial. As the group is distracted, a mysterious black smoke (the demon) sneaks away from the dead body.
Magnus heals the scars on Raphael's face. Aldertree has given him 12 hours to find Camille or else he'll burn down his entire clan. The box hidden at Camille's place, which Simon found, was a box of her grace dirt. The dirt will help them locate her.
A Shadowhunter has been killed at the Institute; they've deduced the demon has broken in. The Institute is on alert and the group splits up to find the demon. Isabelle gives Clary advice about her situation; she doesn't want her friend to leave.
The demon is hiding inside Raj. He tries to kill Lydia, but she fights to defend herself. Alec steps in and forces the demon out of Raj.
Jace is brought in front of the grounds and Aldertree for judgment. It is time for his trial.
Clary tells Jocelyn that she doesn't want to go to Idris. She wants to stay at the Institute with her friends.
After a few truthful questions, Jace admits that he can't follow the Clave wholeheartedly. Aldertree condemns Jace to a life behind bars in the City of Bones. Jace tries to defend himself, but he's apprehended.
Magnus summons Camille to his apartment. He traps her inside a cage.
Clary finds Alec covered in blood. She steps into the next room and finds her mother dead with a hole punched through her chest. Clary is mad and wants the demon dead.
Magnus reveals that he can't have children. Camille demands he choose her and be with her, but he sides with Simon/Raphael and sends her to Idris.
Valentine murders his way through the City of Bones to get to Jace. Valentine was the one who set up the demon at the Institute as a distraction. He kills Hodge and has kidnapped Aldertree to free Jace from his call. The trip was also to steal the Mortal Sword. Dot jumps in to stop Jace from killing Valentine.
Instead of stopping Valentine for a final time, Jace saves Aldertree instead. Valentine runs off with the sword.
Isabelle is possessed by the demon. She fights with Alec, but Clary stabs her in the shoulder to expel the demon. She defeats it and Isabelle is saved. Clary is heartbroken over the death of her mother.