Everyone is dealing with the loss of Clary and are trying to move on best they can. Unbeknownst to them, the Shadowhunters face a new level of evil that they can't even imagine with the arrival of Jonathan Morgenstern, the true form of Clary's brother. With the loss of Clary after Lilith's apartment exploded, Alec, Isabelle and Jace try to come to terms with what has happened. Glad to have their brother back, Alec and Isabelle are still worried about Jace, who is taking the actions of The Owl very hard. Magnus is also mourning the loss of his magic and finds himself in a new position - having to rely on others for help. Meanwhile, Maia tries to help a devastated Simon who has lost his family and his best friend. But unknown to everyone, Clary is alive and finds herself in a new and dangerous predicament.

Jordan and the Praetor try to track down Heidi, while the Shadowhunters try to locate Jonathan. Meanwhile, Luke looks to Maryse for help and Isabelle gets a possible lead on information on what is really going on in the Clave prisons.