Once at the underground entry into the City of Bones where the Silent Brothers lie, Jace reveals that Simon cannot enter into the City of Bones because he is not of Shadowhunters blood. This means that Clary must entre with Jace, however Isabelle gives Simon company in his van parked nearby while Alec circle the area to make sure no demons or other creatures attack.
While in the clutches of the Silent Brothers, Clary is shown memories and a horrible truth showing that her real father is Valentine. This shakes Clary to the core as she runs out of the City of Bones. We jump to Chernobyl which is where the rebellion Circle lies, here we see Jocelyn and Dot, who were attacked and taken there. Dot tries escaping however she fails after she attacks one of the Circle members and is caught by Valentine.
When Clary and Jace emerge from the City of Bones, they find Alec and Isabelle but no Simon. In hysterics Clary runs to the van screaming his name until a voice from above calls out to her. Behind them are two Vampires dangling Simon from high above by his feet. Jace threatens to attack however he cannot due to the accord laws which are laws for downworlds (aka Vampire and Shadowhunters) to follow. This is because they have not broken any laws but are negotiating for the Mortal Cup. The Vampires take Simon and we are left with a cliff hanger to the next episode.