Clary convinces Simon to stay with her and Jace. The three of them enter the church where Jace draws a rune into his arm so that Simon can enter The Institute.

Simon is fascinated by what he sees. Jace goes to a computer screen. The NYPD shows up, but Jace tells them the cops won't discover them. Alec questions why Simon is there.

Jace has an idea of who might be able to help them find out more about Jocelyn's disappearance. Simon can't enter where they are going because the runes on the floor will kill him, so Izzy tells Clary she will take care of him.

Jace takes Clary to the training room.

In a parking garage, a woman is following a guy who has horns coming out of his head. Before she can grab him, Luke grabs her and pulls her behind an SUV. He wants to know about Valentine's plan. A fight ensues, but we only hear a growl, and the truck being pushed back with great, unseen force.

In the training room, Jace and Clary talk to Hodge Starkweather. He gives them information about The Circle and the dangers of Valentine. He tells Clary she must save her mother and get The Mortal Cup before Valentine does. Clary discovers her mother was a member of The Circle.

Clary is upset and more determined than ever to find her mother. Jace thinks Clary's  memory has been wiped. She tells him about Dot and the portal. She learns that Dot is a warlock, and that they have to find her. She might have answers to where her mother might be.

Luke is in Clary's apartment boxing up her things. Dot shows up. She tells Luke she sent Clary to him through a portal. He tells her he's boxing stuff up so to prevent people from tracking Clary. Dot says she's going to see Magnus to find out what he might know about Clary.

Izzy brings Simon some breakfast. They are in her bedroom. She tells him about runes. He asks a lot of questions. She tells him how dangerous The Circle and Valentine is.

Back at the computer screen Jace is trying to find information about Jocelyn, but the information is restricted.

In Valentine's lair, Joceyln is still under a spell.

At police station, Luke is putting things into a drawer when the captain shows up. She asks about Clary and tells him that she was here the other night. He is surprised but plays it off. 

Clary is in Izzy's bedroom, changing clothes. Izzy gives her a pep talk about how this is Clary's destiny. She also tells Clary that her and Jace aren't a "thing."

Back at the station, Luke tells Alaric that they need to find Clary fast.

Dot finds Magnus at the Pandemonium. He's sending warlocks through a portal. She asks for his help, but he declines and encourages her to leave with him. He tells her that Valentine is hunting warlocks. She declines saying she must find Clary.

Simon tries to convince Clary to leave, but Clary resists. Izzy and Jace show up and interrupt them. Then Alec shows up and tells them that The Clave doesn't approve of the mission. Clary wants to know if anyone has a better idea. She grabs the stone on her necklace and has a vision. She sees Dot running from the Pandemonium.

Dot is leaving the Pandemonium when she is attacked by one of Valentine's men.

Clary is running through the Pandemonium searching for Dot. She grabs her necklace again, but no vision. Dot is gone.

Jace suggests they visit the Silent Brothers. Alec and Izzy aren't fond of the idea. Jace explains who they are and how they can help Clary with her memories. He explains the dangers. Clary is all for it, even if the process kills her.

The group travels to the City of Bones, which is beneath a bridge, in Simon's van. Simon questions Clary why she is doing this. Alec and Jace go to see if things are safe. They talk about the dangers and that  if something happens to her, it will be on them.

Simon asks how she is not freaked out by everything. She tells him that she always felt that something was missing.

All of them walk towards the City of Bones.

At Valentine's place, Dot is locked up in a cage. He wants her to reverse the spell. She says it wasn't her. He wants to know who it was. She doesn't say anything. he threatens her and injects her with serum to help her "remember."

Jace tells Clary about the Silent Brothers and the soul sword and that it might kill her if she's not strong enough. She's not afraid. She'll do anything to find her mother. When they get to the entrance, she tells Simon she's scared. He encourages her and she continues.

Only Jace and Clary enter the City of Bones. Simon, Alec, and Izzy stay outside the entrance.

At the police station, Luke is looking through the cups when the captain shows up. She shows him pictures of the two witnesses who were killed. Luke says it must be part of the demonic murders. 

Alaric shows up and the two talk about the murders. Luke tells him finding Clary is imperative.

Clary and Jace walk through the City of Bones. He has a witch light. They come across a statue of a warrior carrying the Mortal Cup. 

Jace shares information about his family.

They come across the clairvoyance circle. The Silent Brothers appear. Brother Jeremiah talks to Clary, tells her to enter the circle. 

Simon tries having a conversation with Izzy and Alec. Alec isn't interested. Simon and Izzy talk about his band. He asks her if she wants to hear some tracks, so they head back to the van where he left his phone. Izzy hears something and tells Simon to stay in the van. He puts on his headphones and something grabs him from behind.

In the Clairvoyance Circle, the soul sword touches Clary's forehead. She has a flashback to when she was young. Luke and Jocelyn are talking about Clary being a Shadowhunter. Jocelyn is afraid. She doesn't want Clary to know that Valentine is her dad.

The flashback stops. Brother Jeremiah tells them that he was only able to retrieve fragments of her memories.

Clary is upset. She tells Jace what she saw. 

In Valentine's lair, Dot uses magic to break out of the cage, but one of Valentine's men attacks her. She's able to injure him, but she's injured as well. Valentine shows up and kills his man, then kills Dot.

Clary and Jace come out of the City of Bones. Clary asks about Simon. Izzy tells them he's gone. Up on the bridge, a vampire wants to exchange Simon for the Mortal Cup. When he finds out they don't have the Mortal Cup, they take Simon and disappear.