Trama

Clary and Simon familiarize themselves with the Institute and learn more about the Circle and the hidden world. Clary has visions and tries looking for Dot, who can get her memories back.

With the knowledge that Valentine is alive and on the hunt for The Mortal Cup, the Institute is on high alert. Not wasting any time, Jace jumps into action and figures Clary's memories are the key to finding Jocelyn and The Mortal Cup. Unfortunately, Clary's memories were wiped leaving her without any recollection of this other life that could help her and the team. With only one other option remaining, Jace, Isabelle and a very reluctant Alec take Clary to the City of Bones to face the powerful Silent Brothers. Meanwhile, Luke continues his search for Clary, and Simon tries to come to terms with his best friend's new life.

The episode takes off at the same point in time where the previous episode ended.

While Simon wants to take Clary away, Jace insists on taking her into the abandoned church / Shadowhunters HQ. In the end all three of them enter and Jace casts a rune to reveal HQ to Simon.

Jace and Alec tell about the Circle revolt against the Shadowhunters, leading to the death of Jace's father amongst others. Jace then takes Clary to the training room while Simon is entertained by Isabelle.

A dark-skinned female Circle member walks in a parking garage, intent on attacking a Warlock. Luke intercepts and threatens to kill the woman. The camera then shifts away; a struggle and growling are heard.

Jace introduces Clary to Hodge Starkweather, former Circle member. Hodge knew Jocelyn (Clary's mother) from the Circle. He is cursed with a rune that tortures him every time he reveals a Circle secret. Hodge also tells about Valentine's plan which would kill many humans. According to Hodge Valentine Morgenstern has died in a fire, and the Mortal Cup can be used to create more Shadowhunters. Hodge states the mission to be to "Stop Valentine."

Jace and Clary conclude that her memory has been wiped by a Warlock, a being described as "half-human, half-demon" and identifiable by a sparkling glow between their fingers (like Dot had, for example).

Dot meets Luke in Clary's house and discusses the current whereabouts of Jocelyn and Clary. Dot mentions involving Magnus Bane, the warlock.

Isabelle and Simon discuss Runes and Isabelle mentions "Forsaken": humans who were given Runes and who did not die, but went crazy.

The captain mentions Clary's presence at the police station a few days earlier to Luke and he discusses the possible overhearing of him talking to Circle members with a co-worker.

Simon tries to persuade Clary to leave the Shadowhunter HQ, but Clary refuses. A little later she clutches her pendant and receives a vision that indicates Dot is at the Pandemonium club. The camera switches to Pandemonium (which is owned by Magnus Bane). Many warlocks are using a portal to get to safety while Dot tries to convince Magnus to help her. Magnus refuses and takes the portal. Outside Dot is captured by Circle members. Clary watches the capture in vision.

Jace mentions the "Silent Brothers", shadow-hunters who can restore memories. After some discussion the group (Jace, Alec, Isabelle, Clary and Simon) drive in Simon's van to the "City of Bones", a subterranean mausoleum for Shadowhuntrers.

Dot has been taken to Valentine Morgensterns headquarters in Chernobyl and locked in a cage. Valentines offers Dot her freedom in exchange for Dot reversing the sleep spell applied to Jocelyn and, when she refuses, injects her.

Jace tells Clary the Silent Brothers can use the Soulsword to carve the truth from someones mind. They then enter the City of Bones.

In the police station the captain shows Luke a picture of the demon killed by Jace outside Shadowhunters HQ and identifies him as one of the two "witnesses" who spoke with Luke a few days before at 2AM. The other "witness" (the dark-skinned woman who battled Luke in the parking garage) has been mauled and deep scratches are visible in a car bonnet. Luke then explains to his coworker that he acted in self-defense, implying he mauled the woman and created the scratches.

In the City of Bones Clary is shown an angelic being holding a cup and a sword; the Shadowhunters crest reads "Nephilim Facilis Descensus Averni" (for Shadowhunters, the descent into hell is easy). After a seemingly short walk in the City of Bones they arrive at a rune which stands for clairvoyance. The six Silent Brothers (whose eyes and mouths have been sown shut) arrive and communicate telepathically to Jace and Clary. They warn her of the Soulsword but Clary goes ahead anyway.

Back near the van, Isabelle and Simon talk and Isabelle offers to listen to some of Simons music. She hears a noise and leaves to investigate, instructing Simon not to leave the van. While listening to some of his music Simon is grabbed by a pair of hands from behind.

The Soulsword only grants Clary one fragment of her memory: a flashback in which Luke and Jocelyn discuss that Valentine Morgenstern is Clary's father.

In Chernobyl Dot uses her magic to break the locks on her hands and her cage. She talks to the sleeping Jocelyn and is then attacked by a Circle member. Dot injects the Circle member with a syringe she grabs from a table; the circle member is then killed by Valentine. He then moves to kill Dot.

Jace and Clary report to Alec. They then discover the disappearance of Simon. They then see Simon hanging upside-down; he has been kidnapped by vampires who want to exchange him for the Mortal Cup. According to Alec, attacking the vampires would violate the Accord. The vampires then disappear.