After all the running around, the shadowhunters finally have the Mortal Cup inside of the institute. Alec wants to hand it over to the clave but Clary is insistent that they cannot do this because it's the only leverage they have over Valentine, who is holding her mother hostage. Alec locks the Mortal Cup away for now but makes it clear to Clary that this is no way means that they are friends. I wish that they would stop having Alec come across like a jealous ex girlfriend, even if this is the tone the books took.
The alarms go off at the institute and Izzy, Jace, Clary and Alec head outside to find out what set off the wards, they find Raphael holding what appears to be an unconscious Simon. Clary is absolutely pissed and blames Raphael for what happened to Simon, completely ignoring that she has spent the last little while blowing Simon off though he called her repeatedly for help. They don't have time for Clary's angst and guilt however because a choice has to be made. Simon either has to be staked to let his soul free or they have to turn him into a vampire. Jace rightfully finds the idea of Simon as a vampire ridiculous and Clary starts to cry.
Lydia Branwell walks into the institute disguised as Valentine. Alec shoots off an arrow very quickly and Lydia catches it and transforms into herself, snarking about the slow response time from the rest of the shadowhunters. Lydia is the representative the Clave sent to see exactly what the Lightwoods have been up to. There's no love between Maryse and and Lydia though their families have a very long history. When Lydia learns that there's been an attack at the werewolf headquarters she decides to check it out with Alec.
Clary has a decision to make about what to do with Simon and so she heads to his home to speak to his mother. Elaine is all distraught about her missing son, and she questions if Clary knows where Simon is. What Elaine doesn't know is that Jace is in the room and he's used a rune to make himself invisible. When Clary starts to hedge and it looks like she is going to reveal how the world really works to Elaine, Jace drops a carved wooden monkey which was a mother's day gift from Simon on the floor. When Eliane walks over to pick up the carving, Jace questions what Clary is doing and tells her to be careful. Umm did anyone see them use a silence rune? If not, how is it that Elaine didn't hear at least Clary's side of the conversation?
Clary heads to Simon's room to collect things that he's going to need for a transition. Jace decides to tell her a story about his childhood. It seems that as a child, Jace's father gave him a falcon to tame. Jace worked with the falcon on a daily basis even though it often drew blood until the falcon trusted him and performed at his command. Jace then took the falcon to his father, who promptly snapped the birds neck. Jace says that he was told to tame the bird and not love it. Jace tells Clary that as a Shadowhunter, she has to learn to think with her head and not her heart and that is what his father taught him by snapping the bird's neck. Clary however is certain that if that is what being a Shadowhunter is all about, she's not interested. Since Clary doesn't make a habit of thinking with her brain anyway, it wouldn't have worked.
On the way to meet with the werewolves, Lydia gets her flirt on with Alec, saying that she knows why so many girls are into him. Alec tactfully ignores this comment. Lydia then reveals that she was going to run the Lisbon institute with her fiancee but he was killed. Lydia then suggests that Alec avoid love. Everyone is filled with happy stories this episode it seems.
Inside the restaurant that the werewolves use as their headquarters, Lydia and Alec find Luke. It seems that the werewolves were attacked by something called a Forsaken. They are all certain that this is the work of none other than Valentine. Luke is certain that this attack is personal and suggests that he might be going after former circle members. Lydia then has a big revelation for Alec - his parents are former members of the circle. She pretends like she is shocked that he didn't know but it's quite obvious that Lydia was aware of Alec's ignorance. Lydia does however promise extra protection for the former circle members.
The Forsaken is taken back to the institute and Lydia decides that the body needs to be checked out by the highest ranking warlock, Magnus Bane. After the autopsy, Magnus delivers the results to Alec though he is disappointed to see Alec put his shirt back on. Alec is clearly not himself and is disappointed by the secrets his parents have been keeping. Magnus advises Alec that he should do something for himself and follow his heart. At this point the shippers and the fans of the series were probably hoping for the first kiss between Magnus and Alec but it didn't happen. The shippers are going to have slow their roll because Alec follows Magnus's advice and proposes marriage to Lydia, so that his family can continue to control the institute. How is this following his heart? Also putting a gay character into a straight marriage is a very big problem.
Clary heads out to a gaveyard with Simon who is being carried by Jace and Raphael. Camille shows up to stake her claim on Simon, saying that all they have to do is get rid of his body to get rid of the proof that she broke the Accords. When Clary, Jace and Alec don't give up, Camille calls in the reinforcements. Raphael makes his play to overthrow Camille, pointing out that she put them in danger by breaking the Accords. Camille tries to blow this off like it's no big deal but the vampires side with Raphael and take her out. Raphael then presents Clary with her two choices: a stake and a shovel. Clary grabs the shovel and starts digging.
Doing some lab work, Izzy realises that the Forsaken has angel blood in him. In the meantime, the Forsaken has attacked Hodge, and seems to be holding his own no problem. Alec intervenes and manages to shoot off two arrows before getting knocked over. Hodge gets up and takes out the Forsaken, as Izzy rushes into the room. Well, it seems that the shadowhunters have a new concern because Valentine can create creatures which can enter the institute and doesn't have to come himself.
Simon pulls himself out of his grave and immediately hisses at Clary and Jace. A calm Raphael tosses Simon a few blood bags and he gulps them down. Simon realises that he cannot say the word, God and assumes that he has become an abomination. Clary tries to tell him that he is the same person that she has always known and is still her best friend. Simon cannot get over the horror of being a vampire and takes off warning Clary to stay away from him. Raphael promises to look after Simon and then takes off after him.