Raphael catches up with Simon who is not happy that he has become a vampire. He blames Raphael and throws him against a truck then runs away. Clary and Jace show up. They decide to keep looking for Simon.
Jace gets a call from Izzy who tells him about the attacks. Jace goes back to the Institute while Clary teams up with Luke to find Simon.
But before they go their separate ways, they have to have a moment and a long kiss.
Magnus is drawing wards to protect the Institute. Alec is watching, but gives Magnus the cold shoulder when he tries to help heal him.
Lydia arrests Meliorn for stealing state secrets and giving them to Valentine. Izzy is not happy about this and confronts Lydia telling her that maybe the reason the Forsaken had Seelie blood was because Valentine had killed Seelies. Lydia doesn't agree.
Alec is angry about his parents and their lies. Jace learns that Robert and Maryse were members of the Circle. Jace doesn't believe them. Lydia introduces herself to Jace. She tells Izzy and Jace about her engagement to Alec.
Simon is home. His mom hugs him and he almost attacks her, but Clary shows up. She takes Simon away.
Alec tells his dad he knows he was a member of the Circle. He is still angry and declares that he will be the one to restore the Lightwood name.
Clary tells Simon she made the choice. He is beyond angry.
Jace, Alec, and Izzy are watching Meliorn's interrogation. He tells Lydia that Clary has the Cup.
Clave members start ransacking Clary's room. Alec tells Jace if Clary doesn't hand over Cup, he will. Jace agrees to find Clary to get it taken care of. Jace warns Clary the Clave is looking for her.
Clary, Simon, and Luke go to the Hotel Dumort for safety. Luke is not allowed in.
Jace tries to convince Alec to make a better choice in regards to Meliorn instead of sending him to the Silent Brothers.
Jace and Izzy go to Magnus for help to get the Cup without Alec knowing. Magnus agrees.
Raphael locks Clary and Simon in a cell to protect them.
Clary tries to justify her choices, but Simon has had enough. Raphael finds it amusing.
Magnus transports Alec's stele so Jace can open the secret safe where the Cup is. Alec comes out of his room to find Magnus there. Alec tells him he is getting married. Magnus is pretty much speechless.
Izzy and Jace try to leave the Institute to get to Clary but are stopped by Hodge who lets them go, but something seems off about him.
The Clave is taking Meliorn to the Silent Brothers. Alec is unsure, but Lydia tells him the story of how her fiance died by making wrong choices. Alec is all in.
Clary hasn't stopped talking to Simon. Izzy and Jace show up to retrieve Cllary and Simon. Izzy tells them they are going to save Meliorn.
Clary wants to form an alliance with the vampires. Simon agrees to become part of Raphael's family and the vampires agree to join Clary's alliance.
The werewolves, vampires, and the three shadowhunters go to the City of Bones to retrieve Meliorn. Luke and Raphael have a confrontation, but Clary stops it. Jace and Clary have another moment.
Alec shows up with Meliorn and some shadowhunter bodyguards. The other team works together to get rid of the guards leaving only Alec and Meliorn.
Jace and Clary confront Alec. Clary takes off with Meliorn. Alec and Jace fight which ends with Alec holding a knife to Jace's throat. He lets Jace go. Jace tries to convince him to break away from the Clave's plan. Alec refuses.
Everyone is at the Hotel Dumort. Simon and Clary have a mushy goodbye. Izzy and Meliorn are locking lips outside. Izzy goes back to the Institute. Clary and Jace are going to take Meliorn to a Seelie court.
Meliorn thanks Clary for saving him and tells her how she can find Valentine.