ack on Valentine’s ship, Jace is annoyed that Valentine set him up to kill the vampire. Valentine pulls the arrow out of his shoulder, testing Jace's anger and reminding him that he could transport them via a portal to Idris and straight to the Clave but instead Jace took them back to the ship.
Escorted back to the Institute, Clary is angry at her mum Jocelyn for shooting an arrow at Jace and she wants answers. Jocelyn tries to explain to Clary that she did that for the right reasons. Clary doesn’t understand causing Jocelyn to explain that, when she was pregnant with Jace, Valentine injected Jocelyn with demon blood and experimented on Jace before he was born. Clary still doesn’t believe her and so Jocelyn shows Clary a memory of Jace when he was a baby in Jocelyn’s arms as he turned a living flower into nothing.
Clary and Simon are now in Clary's room at the institute. Simon is waiting to be called upon to be questioned about that night’s events. However, Clary still doesn’t believe that the Jace she knows could be anything like the baby in the memory. Lydia interrupts them by telling Simon that Aldertree is ready to seem him. However, Aldertree has a different motive to wanting to see Simon. Aldertree asks Simon to look into recent events in order to get to the bottom of the situation of vampires feeding off of the mundane. Aldertree threatens Simon stating that, if he doesn’t find out this information, he cannot come into the institute and see Clary.
Clary goes to see Alec; however, he is upset and annoyed that they couldn't save Jace. This causes him to take his anger out on Clary expressing that she doesn’t belong in their world and she will never be a part of the institute. Isabell tries to tell Alec to stop but he doesn’t and the damage to Clary has already been done.
A debriefing starts later on, but no one alerts Clary which causes her to turn up at the end, not happy that she was not alerted. Clary approaches Lydia telling her that she can help but Aldertree interrupts, telling Clary that her lack of training and being close to the situation as Valentine’s daughter and Jace's sister are against her. Aldertree takes to Lydia to one side and reveals that he wants Alec and Isabelle taken off the mission because they are also close to the situation. Lydia stands up for them telling Aldertree that they are the best shadowhunters they have got so they have to stay on the mission.
Clary approaches Isabell and asks her to go with them, however, Alec reinforms Clary that she is not one of them, and then turns to Isabelle asking if she's ready to go. Clary now feels isolated from those she thought were her friends and despite thinking that she had finally found somewhere to belong to she now feels the complete opposite. Clary begins to look back at her old life and how easy it was then. Isabelle comes into Clary’s room to reassure her that she is one of them and not to listen to Alec. However, Clary believes Alec despite Isabelle’s attempts and she now wants to go back to her normal life. Isabelle reminds Clary that she has a massive target over her head and the institute is the best place for her. Isabelle also reminds Clary that she has her to rely on and that will never change.
Luke is investigating the disappearances occurring at fighting gyms and clubs across New York. However, Luke wants to keep this in their world and away from the mundanes. Alaric wants to know how long Luke is planning to keep Simon in werewolf territory. Luke explains that Simon is going through a tough time at the moment so he is staying.
Simon, when returning to Jade Wolf, is stopped by the werewolves as they don’t want to see him around there anymore. They push Simon into the canoe shed and tell him to stay there. However, Raphael is waiting for Simon inside the canoe shed. Raphael is curious to why Simon told Aldertree that he had something to do with Maria dens. Simon, confused, tries to explain himself but Raphael tells Simon that Camille turned Maria, meaning that Camille controls that den which could lead to Raphael. Raphael threatens Simon and tells him that he now has to find Camille and bring her back to hotel De mort or die trying.
Back at Valentine’s ship, those who are missing from the city are lined up in front of him ready to drink from the mortal cup. Jace approaches one of the members warning him about the wards around the ship. Jace is surprised to see that this member doesn’t see why anyone would like to leave and he cannot wait to kill the downworlders due to one killing his father. Valentine interrupts asking if Jace would to lead a mission into the city to kidnap some downworlders, which Jace refuses to do and walks away. Valentine knows there only one person can convince him.
Back at the institute, Jocelyn goes to see Clary and bring her a cup of coffee however, when she enters Clary room, she is gone and she has left her steelie behind.
Alec and Isabelle enter one of the fighting clubs to start their mission and hope to capture a circle. Isabelle makes a comment on one of the fighter’s form. This fighter tries a pickup line or two on Isabelle but it doesn’t work and Isabelle challenges him to a fight. The fighter, in refusing to fight Isabelle, makes it easier for Isabelle as she defeats the fights leaving him on the floor.
Magnus has transported Simon to his apartment to find out what the emergency is. Simon explains to Magnus that he needs to find Camille and asks Magnus for his help because he knows her better than anyone else. Magnus refuses because he knows that looking for Camille is not a good idea, however Simon convinces Magnus to help him and Magnus, eventually, agrees.
At the fighting club, the arrogant fighter is getting ready to leave, until he his attacked by a circle. Unknown to the audience this is actually Isabelle shape shifted as the fighter. Wanting answers from the circle member, Isabelle and Alec start interrogating him. However, the circle member cuts his throat instead of being taken by them.
Clary is at the Brooklyn Academy of Arts to try and regain some of her old life. Jocelyn is meeting up with Luke and tells him everything, including Jace’s demon blood. Luke is not happy that Jocelyn has never told him this causing Jocelyn to explain why she never told him. Jocelyn explains that she knows where Clary is but she needs Luke to talk to her because Clary will not listen to her mother but she will listen to Luke. Luke agrees to speak to Clary.
Magnus transports Simon and himself to India in order to find one of Camille's many hideouts. Magnus starts collecting his things from Camille's hideout which he hadn’t retrieved after their break up, leaving Simon to find Camille himself.
Clary, still at the Academy of Arts, is sketching the New York skyline in one of the classrooms. She is interrupted by Luke and Jocelyn, who both want Clary to return to the institute because she will be safe there. However, Clary expresses her feeling that she doesn’t belong there and she never will because she is not a Shadowhunter like everyone else there. Clary also expresses that she believed she could have a normal life growing up, reminding Luke and Jocelyn that no one there will trust her because she's Valentine daughter, before storming out of the academy. As Clary is leaving she bumps into Dot, who they believed to be dead, who grabs her arm to drag her through a portal before Jocelyn and Luke could catch up.
Alec is annoyed that they couldn’t capture the circle member but Isabelle reminds him that if Jace was hurt he would be able to feel it. However, Alec is worried because he cannot feel anything and that is what scares him the most.
Simon, on the other hand, is still looking for Camille and he comes across a wired room full of strange things such as a snake statue. When Simon touches the statue a box is released from a hidden compartment, but it is guarded by a snake.
Jocelyn and Luke go to the Jade Wolf. Jocelyn explains that she recognizes the lines on Dot’s face and that Valentine is using the injections again. Lukes thinks of a way to get to Clary by finding Jace. Luke smashes a cat figure and reveals amust which his mother gave to him which cannot track Jace alone.
Back at the Institute, Alec is becoming desperate to find Jace as he needs his para batia. Overhearing, Jocelyn interrupts them and gives them a way to find Jace. Alec is curious as to why Luke didn’t show them amust in the first place. Jocelyn explains that it will not only find Jace but it will also help her find Clary as she has been kidnapped.
Back at Valentine’s ship, Jace is looking over to the city until Clary approaches him. Jace is unsure as to whether this is the real Clary and so he forces her into a choke hold until she reminds Jace of a memory they both share of what happened when they stole a vampire’s motorcycle. Jace is shocked that it is the real Clary and so he asks why she is there. Clary explains that Dot brought her there to show her something. Clary explains what Dot showed her and tells Jace that one day the downworlders will kill the mundane and Jace is the only one who can stop them. They are interrupted by Valentine who asks Jace again about the mission and when Jace refuses for the second time, Valentine asks Clary but before Clary can answer Jace agrees to lead the mission as long as Clary stays safe.
Simon is scared out of his mind because of the snake. He tries to remind himself that there nothing to be afraid of until the snake starts breathing fire. Pulling himself together, Simon uses his vampire powers to control the mind of the snake to send it away. It finally works, however, Magnus has transported himself into the room and finds Simon.
At the institute, Alec is getting ready to use the amust to find Jace, but before they begin Jocelyn warns Alec that he cannot go in too deep because he will find it very hard to get back. Isabelle, upon hearing about this, is not happy and wants Alec to stop before he starts. Alec, on the other hand, is determined to find Jace at any cost.
Back on the ship, Clary awakes trapped in a cell, not knowing where she is. Dot cast a spell over Clary to tell Jace that she can see the future when in reality she can't and it was all a lie. Dot reveals that she has to do it again but Clary stops her asking Dot to help her instead by talking about memories. Dot asks why she stopped looking for her and Clary explains that Magnus couldn’t feel her magic anymore. Dot explains that it was the injection which affected Magnus’ ability to feel her magic because she is weak with the injection. Clary pleas for Dot’s help.
Alec is ready to find Jace and Jocelyn explains that he needs to stay safe above the surface or he won’t be able to come back. Isabelle reminds Alec that if he doesn’t come back she will hurt him when he does. Grabbing the stone Alec focuses on Jace.
Magnus and Simon are back at Magnus’ apartment going through their collection from Camille's home in India. Simon is curious as to how to open the box so they can lure her back. Magnus, however, tells Simon that he didn’t have anyone to show him the way of downworld.
At Valentine's ship, Jace returns with one of the wolves from Luke's pack. Valentine wants Jace to kill the wolf however Jace refuses as she hasn’t done anything wrong. Clary approaches them, bursting out with the truth to Jace of her being under a spell before and to run. They are attacked by some circle members as they run, who defeat them. Alec now sees Jace however this causes Jace to become weak as he can feel Alec. Alec causes his body to have a fight in order to make Jace fight on. Clary grabs Jace as Dot opens a hole in the wards for them to leave through and they both jump into the river. Valentine, annoyed, kills the wolf ending episode two of season two.