First, we catch up with Simon who is running away and freaking out. Raphael finds him and tries to assure/calm him down. Simon refuses and blames Raphael for his transition. He throws him against a truck and takes off. Clary and Jace catch up and question Raphael. He sends them after Simon and says he can only help when Simon is ready to accept it. He also lets Clary know that Simon doesn't know who turned him. Jace calls Alec for help.
Back at the Institute, Alec is being stitched up by his father and Izzy answers his phone. She tells Jace about the Forsaken attack and that this creature had magic and Seelie properties in it's blood. Jace says he is on his way. He tells Clary to get Luke to help her find Simon and they'll figure out the rest later. They agree they need to talk about their relationship, but settle for a kiss instead. Jace arrives at the Institute to find out what's going on. Magnus is there casting protection spells all over the Institute and he offers to heal Alec, but he declines and walks away. Magnus asks where he can find Lydia so they can discuss his payment.
Lydia brings in Meliorn for questioning and Izzy is furious. She demands to know why. Lydia says Izzy should also be arrested for practically committing treason by sharing secrets with Meliorn. They argue and Lydia walks away to interrogate the prisoner. Alec tells Izzy to be paitient and Jace agrees. They watch the interrogation live. Meliorn reveals that Valentine's daughter has the Mortal Cup and Lydia is pissed. She has shadowhunters search Clary's room. Jace and Izzy agree they need a plan. Alec tells Jace he needs to have Clary come in and hand over the Cup, or he'll do it himself. Jace makes him promise to wait until Clary gets there and that he'll bring her back. Alec agrees.
Clary goes to Luke and they track down Simon. Clary tells Simon the truth about who turned him and apologizes. She shares that she just couldn't lose him. She gets a call from Jace who tells her that the Clave knows she has the Cup and she needs to go somewhere they'll never look to find her. Simon runs off again.
He has returned home and his mother is so happy to see him. She holds him and he tries to refrain but he nearly bites her until Clary runs in. She lies and says her identity has been stolen and she needs Simon's help. Ms. Lewis isn't sure he should leave but Clary pleads with Simon who ultimately agrees to help. Clary promises to take care of Simon. They leave and head to the Hotel Dumort. Raphael meets them and Luke outside and the animosity between Luke and Raphael is obvious. Clary tells Raphael that the Clave is looking for her and she needs a place to hide and they also have to protect Simon in order to prove that Camille broke the Accords. Raphael agrees to hide them. He locks them together in a cage, knowing the Simon is starving. He reminds them that they're no longer equals and Simon will always be a downworlder and Clary will always be a Shadowhunter.
Alec agrees with Lydia about taking Meliorn to the Silent Brothers which is basically a death sentence. Jace and Izzy protest, but his mind is made up. He shares that their parents were Circle members who made a deal with the Clave, but now that Valentine is on the loose they can't be trusted. He is clearly very angry and feels like he has been lied to his entire life. They also share the news of their engagement and no one is pleased about it. Izzy and Jace start to put together a plan. They go to Magnus and ask him to steal Alec's steele so they can get the Cup and get it into safe hands. Magnus reluctantly agrees. Magnus gets the steele to Jace who breaks into the vault and gets the Cup and Clary's necklace. Alec tells Magnus about his engagement and he is clearly heartbroken. Jace and Izzy are about to sneak out when Hodge finds them. He questions them, and they come clean. He pretends he doesn't see them.
Clary apologizes again to Simon and he yells. He can hear her heart beat and he wants to drink her blood. He finally yells for Raphael who brings him blood. He feeds and starts to calm down. He tells Clary he's upset, but he doesn't hate her. They promise to be there for each other. Raphael releases them as Jace and Izzy show up outside. Jace and Izzy inform Clary about what's happening with Meliorn and she agrees that they have to stop it, but they'll need help. Luke says the pack will help and Clary says they'll need the vampires too. They go upstairs to talk to them and Clary pleads with Raphael. He says he will agree only if Simon pledges his allegiance to Raphael. Simon agrees and Clary tries to stop him. Simon tells her that this is his role to take in this war. Clary nods and agrees that it's time for all species to become equals.
They go to the downworlder entrance of the Silent City and start their plan. The wolves and vampires almost get into it, after some kind of funny banter, but Clary intervenes. She reminds them that they have to work together or they'll never get this done. Slowly, they work together taking down the Shadowhunters escorting Meliorn. Clary and Jace realize Alec is also with him and they hope they can reason with him. Alec brings Meliorn to the entrance and Clary begs him not too. He disagrees and Jace intervenes. He demands to know what is going on and Alec is pissed that Jace is suddenly breaking the rules because of Clary. They start fighting and Clary and Meliorn take off. Jace yells that he knows why Alec hates Clary so much, that it's about him. Alec flips out and they fight until Alec pulls his seraph blade on Jace. Jace tells him to do it, because he doesn't want to live in a world where they're on opposite sides. Jace asks Alec to come with them so they can find Valentine and fight him the right way. He begs him as his parabatai to come but Alec refuses and Jace leaves.
Meliorn can't believe that everyone worked together to save him and that the shadowhunters orchestrated it. The vampires go back to the hotel and the wolves go back to the Jade Wolf. Izzy kisses Meliorn before returning to the Institute to find out what's going on. Meliorn thanks Clary for all she did and offers a gift. He tells her he can help her find Valentine.