Alec wants to turn the Cup over to the Clave, but Clary and Jace convince him to keep it at the Institute as a way to help find Clary's mother. Alec hides the cup in a rune protected vault in the floor.
Clary is trying to call Simon, but can't reach him. Jace is annoyed.
The Institute's alarms go off as its perimeters appear to be breached. Alec and the others go out to investigate. It's Raphael holding Simon who is dead. They bring Simon into the basement of the Institute. Raphael tells Clary she either has to stake him (and he dies forever) or bury him (and he becomes a vampire forever), but she has to decided by sunset.
Valentine is talking to greeb blob encased Jocelyn. One of his soldiers show up with two zombie-like guys who are foresakens.
Robert and Maryse tell Alec and Izzy that a Clave envoy is arriving.
Alec is talking to Max, asking him to stay out of trouble, when Valentine shows up. He shoots his arrow, but Valentine catches it. It turns out that it was Lydia Branwell, the Clave envoy.
She wants to know where Clary is, but Alec tells her he's out with Jace.
Valentine's henchman and two foresaken show up at the Jade Wolf. A fight ensues. One of the foresaken is killed by Luke.
Jace and Clary are at Simon's house. Clary wants to tell Simon's mom that Simon won't be coming back. The mom can't see Jace. Clary tells her some story that we didn't see onscreen. Clary is in Simon's room gathering up his things and arguing with Jace. He tells her a story about a falcon and emotions.
Alec gets a call from Luke regarding the attack. Lydia and Alec go to the Jade Wolf. They take the foresaken's body back to the Institute.
Alec learns that his parents were members of the Circle.
Lydia and Alec are examining the foresaken in the autopsy room of the Institute. She tells him they need to bring in Magnus to do an examination. Alec starts talking fondly about Magnus.
Clary and Jace show up at the Jade Wolf where Clary tells Luke about Simon's death and asks for his advice. He just tells her to be careful if she decides to resurrect him. He shares his transformation to a werewolf story.
Magnus and Izzy are in autopsy room. Apparently Izzy is the renowned pathologist. Magnus is asking about Alec while Izzy starts dissecting the body.
Alec is working out when Magnus comes in with the report of his findings from his portion of the autopsy. Alec spills his guys about his parents.
Clary has decided to take Simon to the cemetery. She's there with Raphael and Jace. Camille shows up and demands they hand over Simon, because he is her property. Raphael challenges her. Clary slaps her, and the vampires she brought with her, turn on her. Raphael is now in charge.
Lydia tells Maryse and Robert that the Clave will be taking over the Institute. Alec overhears when he is about to deliver the report.
Clary chooses to bury Simon so he can return as a vampire. She's very upset.
Alec talks to Lydia and suggest they marry in order to become stronger allies, but also it will allow them to clear the Lightwood's name and take back control of the Institute.
Simon wakes up and claws out of his grave. Raphael has bags of blood for him which he greedily slups down.
Izzy discovers that the foresaken has angel blood. She runs to share her discovery. Hodge is working out when the other foresaken attacks him. Alec comes in to help, but is quickly taken down. Hodge saves the day. Izzy comes in at the end.
Simon has calmed down and slowly realizes what he has become. He is repulsed by the idea and runs off. Raphael tells Clary he will look after Simon and takes off after him.