Clary's phone goes off and they all run to the operation center. Maryse is now back from Idris, however she is not alone. Maryse makes an announcement to the whole of the institute about Valentine and Jace. Maryse announces that there is a new head of the Institute as Lydia was deemed unfit by the Clave and has been replaced by Victor Aldertree. Victor Aldertree wants to find Jace by interviewing everyone who went on the last mission with him and he also wants to turn the Institute around. He does this by putting the Institute on lockdown.
On Valentine’s ship Jace is changed up whilst taking a beating from one of Valentine’s experiments. This is because he is still killing Valentine in training, and is still not loyal. Valentine wants to speak to Jace so he runs a steelie over one of Jace's ruin and tells him to get dressed.
Clary goes to Aldertree for her interview about Jace. Aldertree explains that it is an official interview which he has to record for the investigation. Aldertree asks about their last mission together, however Clary is too honest about the mission.
Valentine, on the other hand, is cooking in the ship’s kitchen. Jace joins him but he still doesn’t trust Valentine which causes him to pick up a knife and attack Valentine. Valentine intercepts it, stopping Jace from killing him. Valentine talks about old memories from when Jace was little and he was glamoured as Michael Wayland. Jace becomes defensive until Valentine shows Jace a memory of his. Jace learns that Valentine experimented on him before he was born and injected demon venom into him when he was in Jocelyn’s womb.
Magnus has now finished his interview with Aldertree and doesn’t believe he can help anymore so he leaves, but he is spotted by Alec leaving. Alec asks why he's leaving and why he doesn’t want to help. Magnus cannot deal with Alec being stressed right now, however an alarm is sounded and Alec goes into the operation room and sees that Clary and Isabell are there already. They cannot believe that Aldertree has put a warrant out on Jace's head and wants Jace dead or alive as he believes Jace is a traitor to the Clave. Clary and Jocelyn are both still on lockdown because they are related, or had a relationship with, Valentine. However, the rest of the Institute is not on lockdown anymore. Aldertree also announces that all downworlders are banned from entering the Institute without his approval and demands that Luke and Simon leave the Institute immediately.
Luke and Simon leave and both return to the Jade Wolf where Luke explains that Simon can stay there as long as he needs and that Aldertree is not the problem: the Clave is. Simon is worried about Clary as he believes Valentine will come for her next. Luke's phone rings and he leaves Simon alone. Simon is approached by the other wolves who demand that he leaves the Jade Wolf. They force him out into the canoe shed outside the Jade Wolf. They lock him in and tell him never to come out.
On Valentine’s ship, Valentine and Jace are looking over his followers in training. Valentine explains his reasons for experimenting on Jace. Jace, on the other hand, has the idea of going overboard but Valentine stops this by throwing a downworlder over the edge revealing the wards surrounding the ship as it burns the side of the downworlder’s face.
Isabell takes Clary into the training room to train her to fight. Clary is not happy that Isabell would apparently rather train than look for Jace. However, as they train Isabell explains that if she looks for Jace Aldertree has threatened to de-ruin her. Clary, picking up the fighting technique very quickly, leaves the training room after putting Isabell on the floor. Alec is caught by his mother, Maryse, leaving the Institute. Alec and Maryse argue about Jace and how he is not Alec’s brother to Maryse, but to Alec Jace is his brother. Alec walks away from his mother and the Institute, heading to Magnus's.
Aldertree arrives at the Jade Wolf asking for Luke's help. However it is revealed not to be Aldertree but actually Clary glamoured as Aldertree. Luke tells Clary that he will help her to find Jace and that Simon is in the canoe shed still. Clary goes to see Simon and Luke rings Jocelyn to tell her that Clary is with him at the Jade Wolf.
Clary, with Simon, is trying to track Jace but is having no luck until they are interrupted by Jocelyn. Clary is not surprised that Luke contacted her about her whereabouts. Jocelyn offers her help to find Jace, however Jocelyn asks for Clary’s phone and steelie because she has a way to track him. However, Jocelyn isn't telling the whole truth as she leaves Simon and Clary in the shed and locks it.
Alec is now at Magnus's, despite the fact that Magnus is still upset with Alec. Alec tries to apologise to Magnus about taking his anger and stress out on him. Magnus reminds Alec that they are going to face tough times and that Alec cannot push Magnus away when it happens. He needs to trust Magnus that everything will be okay.
Simon and Clary are still locked in the canoe shed. Simon tries to run at the door with his vampire strength to open it, but it is not working. Clary and Simon sit and talk about old memories and how much their lives have changed over the last few weeks. Interrupting them, the door falls to the floor allowing them to leave.
Jocelyn, on the other hand, is tracking Jace and Alec is about to start to track Jace through their parabatai bound, but before Alec starts Jace and Valentine come back into the city. Alec is now able to sense Jace and so he leaves Magnus's, but Alec is not the only one who knows that he is back as an alarm is set off at the Institute. Valentine explains to Jace why they are back in the city, and that is because a vampire called Maria and her clan are feeding off of mundanes. Jace being Jace runs into the building after hearing a scream, he finds vampires feeding from mundanes. After fighting the vampires off and rescuing the mundanes Jace asks for Maria. Alec is now back at the Institute explaining that he and Isabell should be the ones to bring back Jace, but Aldertree disagrees and keeps the held at the institute while others go to retrieve Jace from Valentine.
Continuing to fight the vampire, Jace come across Maria who attacks him leading them outside. Maria surrenders to the clave, stopping Jace from killing her otherwise it breaks the accords. Taunting Jace, Maria goes for an attack but Jace ends up killing her. Clary, Simon and Jocelyn turn up at the scene but it is not looking good for Jace because Jocelyn fires and arrow at Jace. Valentine jumps in front of the arrow and the arrow goes into Valentine shoulder. Clary screaming at her mum to stop, runs to her. Jace grabs Valentine and they disappear into the portal ending the first episode of season two.