Believing the key to find the Mortal Cup lies within Clary's mind, Starkweather instructs Jace to take Clary to the City of Bones, where fallen Shadowhunters are laid to rest, to meet Brother Jeremiah (Stephen R. Hart), a dead Shadowhunter that probes Clary's mind and learns of her
connection to a powerful sorcerer, Magnus Bane (Godfrey Gao). Clary, Jace, Simon, Alec and Isabelle meet Bane in a nightclub, where he reveals that Jocelyn hired him to block knowledge of the Shadowhunters from Clary's mind. Their conversation is interrupted when Simon is kidnapped by vampires, leading to a confrontation in a nearby hotel, in which the group is nearly killed before werewolves that hold a truce with the Shadowhunters intervene and save them.
Back in the Institute, Clary falls in love with Jace while joining him on a romantic evening with him in the greenhouse inside of the institute. Later on in the evening, Jace and Clary share a kiss and head back to her room. As Jace and Cary kiss the second time, Simon interrupts by opening the door, causing an awkward presence for the trio. After Jace leaves feeling confused and angered once Clary says to Simon " we were just kissing ", Simon then confesses to Clary that he loves her and always has. Although, Clary does not respond to this as she is surprised; allowing Simon to feel heart broken, and leaves the room. She eventually realizes that the Mortal Cup is hidden inside a tarot card belonging to her mother, and the group returns to Clary's apartment to retrieve it. There, they discover Madame Dorothea is a demon sent to steal the Mortal Cup. It is killed by Simon and Jace after mortally wounding Alec, while Clary retrieves the Mortal Cup.