Jace is asking Clary about her Valentine vision. He says the necklace is a portal shard. Alec comes in. He wants answers. He takes the necklace. He's worried that Valentine might be able to use it to find the Institute. He hides the necklace in the floor.
Clary is in the hallway. she is upset. Izzy comes to comfort her. She tells Izzy about her mother. Complains about Alec. Izzy tells her he's just trying to protect them. Clary says she just wants to find her mother. Izzy wants to know everything about Clary's mother. They begin walking and talking.
Maryse Lightwood enters the Institute through a portal door. She is not a nice person, and is the complete opposite of how Clary just described her mother. She wants to know where Jace is because there is a "situation." Clary is confused and questions Izzy about her mother.
Maryse is watching Jace training with a sword. Alec comes up to her. They hug. Jace notices she is there. She tells them about the problem of the Seelie's no longer communicating with the Clave. Izzy says she has Seelie friends so Maryse sends her and Jace to find out what's going on. She puts Alec in charge of taking care of Clary.
Luke is at the police station, looking at papers and playing paper basketball. Alaric comes in and they talk about the demonic murders. He mentions something about mundanes with the sight. Alaric tells him that the werewolf can't afford for Luke to lose his badge, so Luke tells Alaric to find Clary.
At the Institute Clary is drawing a sketch of Valentine. When she finishes, she rips it off, crumples it, and throws it away.
Jace and Alec are talking. Alec says he'll babysit Clary while Jace goes on his mission. Alec thinks that Jace is upset with him about the Magnus reveal. Jace tells Alec that he knows he loves him, but he thinks it's parabatai love. Alec drops it. Jace implores Alec to watch over Clary while he's gone.
Simon is outside the Hotel Dumort when Raphael shows up. He threatens Simon and makes him leave.
Clary is in the training room with a training stick. Alec comes in and starts to work with her. They have a conversation about Maryse, Jace, and other things. It's an intense conversation, but Clary still needs work.
Clary is challenging Alec. She tells him about a box that her mother had that belonged to her father..the father she thought was her father, not Valentine. She tells him that they should go get the box which is at the loft, but Alec isn't sure.
Alec's phone rings. It's Magnus. He asks Alec for a date. When Alec turns around, Clary is gone. He tells Magnus he has to go and takes off to find Clary. She is not in the Institute.
Magnus is not deterred. He makes it clear, he'll keep trying.
At the Jade Wolf, a wolf comes in. There are a bunch of men talking. Theo, the leader, tells the wolf he's late. The wolf goes in the back and transforms. It's Alaric. Theo gets up and starts talking about shadowhunters and how they shouldn't be trusted. He wants them to hunt down Clary so they can get the Mortal Cup.
Clary is outside the Brooklyn Academy of Art. Everything is moving in slow motion. She has an invisibility rune on her. Her phone rings, and since no one can see here, people are looking at their phones. Alec finds her. Clary picks up the phone. It's Simon.
Clary tells Simon about the memory demon and says she's going to the loft. Simon says to go the shortcut way and he'll meet her there.
Alec is not thrilled with any of it, especially involving Simon again. Clary confronts Alec on his homosexuality. She says she knows that he's in love with Jace. He counters that he knows she's in love with Jace. It's a standstill.
Jace and Izzy show up at Meliorn's place. Meliorn is doing a little bit of praying.
At Valentine's lair, he has a group of guys that look like prisoners. He is talking to them about making the ulitimate sacrifice. One comes forward and he burns a circle in his neck, then one of the henchmen injects him with something that causes the guy to pass out. Valentine says if he's strong enough, the guy will live. Whatever that means.
Near the loft, Simon and Clary catch up. Clary lays out her plans. Simon is showing some vampire abilities like swiftly jumping over a wall. Alec continues to be a buzz kill.
Outside the loft, there are lots of runs burnt into the building. Simon can see them. Alec questions that, but that's all he does. Clary points out the heart they once drew on the wall and talks about how they were once engaged. Alec isn't amused. Simon is sad.
The loft is locked and Simon easily opens the door. He is displaying extraordinary strength.
Simon finds loose floorboards. The box they are looking for is there. Clary doesn't recognize anything in the box. There's a noise and Alec goes to investigate. He tells Simon and Clary to stay put, but it was a trap. While Alec is trying to kill whatever is out there (it's a werewolf), the wolves have taken Clary and Simon under the guise of being police officers. Alec figures it out, but he's too late.
At Meliorn's place, Izzy is asking questions. Jace figures out that Valentine killed the Seelie scouts. He tries to convince Meliorn that the shadowhunters are on his side. Meliorn isn't convinced. Jace gets a text from Alec about Clary. He is not happy.
Jace and Izzy show up at the loft. Alec tells him what happened. Jace is extremely upset. So is Izzy.
The werewolves take Simon and Clary to the Jade Wolf on the dock. Alaric gets a call from Luke, but is ordered by Theo to ignore it.
Back outside the loft, Jace is desperately trying to do a track of Clary, but is unsuccessful. He suggests he and Alec do a parabatai track. Jace is so angry that he thinks Alec isn't concentrating, but Alec assures him he is. Izzy tries to calm Jace down, but it isn't working. The parabatai track doesn't work. Jace believes because something is preventing it...like being by a body of water.
Theo starts questioning Clary about the Cup, but she says she doesn't know where it is. Theo doesn't believe her so he orders one of his men take Simon out.
Theo comes back in. He tells Clary that unless she tells him where the cup is, Simon will die. Clary finally figures out that these guys are werewolves. Gee, what gave it away?
Clary lies about the Cup, telling Theo it's in the loft. Theo sends a couple of guys after it. He tells her that if she is lying, she will have Gretl rip apart Simon and he'll make her watch.
Simon is upside down in a holding cell somewhere on the dock, but with his new vampire strength he is able to break out of the cuffs and free himself, though he still doesn't realize he is almost a vampire. He tries to find a way out, but then figures out he can call someone, so he calls Clary's phone.
Outside the loft, Clary's phone rings. Jace picks it up. Simon tells him what happened. Jace asks for information about his location.
While waiting for Jace and the gang, Simon decides to pull a fire alarm. The werewolves leave the Jade Wolf. Theo puts Clary in a container on the dock. She has the witch stone with her. She draws a fire rune on the door. The door bursts into flames, but nothing happens. A short time later, the doors open. it's Luke.
Clary doesn't trust Luke and tells him to leave. He tries to explain he was protecting her from Valentine, but she doesn't believe him. Luke overtakes Clary and throws her over his shoulder, but when he gets outside Jace and gang are waiting for him. They take him out and free Clary.
They are trying to escape, but are surrounded by werewolves. Theo comes out as a werewolf, but Luke who has transformed back into a werewolf attacks him. They fight. Theo is dead. Luke returns to human form, but he is severely injured. He tells Clary he always promised her mother he'd take care of her. Then he passes out.
It gets a bit intense between Jace and Clary, especially when he touches her face. He tells her he will help her help Luke. He says that the only a warlock's magic can cure an alpha's bite. She says they must get Luke to Magnus. Jace agrees. Alec says they need to get Clary back to the Institute, but Jace tells him that he and Izzy should go back. He's staying with and helping Clary.
Jace is very angry with Alec for letting this happen. Simon helps Luke into the car. He's going to drive. Izzy and Alec watch them take off. Izzy asks Alec if everything is okay between him and Jace. Alec can't answer.