The main antagonists in
City of Heavenly Fire are the Endarkened, led by Sebastian Morganstern, who has a secret alliance with the Seelie Queen. The narrative switches between Idris and New York. In both locations, the Shadowhunters and their allies must face the Endarkened threat while struggling with their own personal demons.
The Endarkened storm five Shadowhunter Institutes, leading the Clave to declare an emergency evacuation of all Shadowhunters to a lockdown in Idris. Around fifty Shadowhunters are later sent to repel an attack of around twenty Endarkened on the Adamant Citadel. In the ensuing battle, many Shadowhunters are slain, weakened by the hope that their corrupted loved ones can be captured and cured. The fight ends when the Iron Sisters intervene. Later, Meliorn drugs Jocelyn, Luke, Magnus and Raphael, and hands them over to the Endarkened. When the Shadowhunters and their allies in Alicante assemble for a council meeting, they discover the Downworlder representatives’ chairs empty. On the floor is a message from Sebastian, written in angel blood: “I have come.” Matthias, an Endarkened, tells the Shadowhunters that if they do not surrender Clary and Jace to Sebastian within two days, the Downworlder representatives will be executed.
Throughout all this, Jace is trying to come to terms with, and control, the heavenly fire in his veins. During the battle at the Adamant Citadel, Jace is wounded by Sebastian, who is injured when the heavenly fire in Jace’s blood sends a spark up the Morgenstern sword. Zachariah, a Silent Brother, tries to tend to Jace’s wound, and is also burned by the heavenly fire. However, far from harming Zachariah, the fire returns him to his original state as a Shadowhunter. Once again the fire emanates from Jace in battle, when he, Clary, Simon, Isabelle and Alec travel to the demon realm of Edom to rescue the Downworlder hostages, who are being held there. In Edom, Jace encounters a demon in the form of Magdalena, the Iron Sister he killed. The demon taunts Jace, playing on his fears that he has evil within him. He vanquishes her by channelling the heavenly fire through his sword, but is encircled by flames himself. Clary is then able to transfer the fire into her recently acquired sword, Heosphoros, an ancient weapon commissioned alongside her brother’s from Wayland the Smith.
Back in New York, Maia and Jordan find the Praetor Lupus headquarters occupied by Endarkened, who have slaughtered many of the werewolves there. Sebastian kills Jordan, but leaves Maia to spread word of the Endarkened’s actions. The slaughter at Praetor Lupus leaves the temporary leadership of the New York pack vacant, and Rufus Hastings begins to foment rebellion among the werewolves, complaining that Luke is more loyal to the Shadowhunters than to his own kind. Bat challenges Rufus to a fight, with the winner taking on temporary leadership of the pack. Just as it seems as if Bat will be slain, Maia takes his place and defeats Rufus, assuming the leadership herself. When Maia is informed that Sebastian has captured the Downworlder representatives, she decides that it is necessary for werewolves and vampires to form an alliance. She tricks Maureen into drinking holy water, causing the vampire to dissolve, thus allowing Lily to take her place.
As the novel reaches its dénouement, Clary, Jace, Simon, Isabelle and Alec infiltrate Sebastian’s fortress. At the same time, the Shadowhunters in Idris try to fend off an attack by a force of faeries and Endarkened, having only just been alerted to the Fair Folk’s treachery. Simon, Isabelle and Alec free the hostages, while Clary and Jace confront Sebastian, who says that he will seal the gates between the demon dimensions and Earth if Clary will rule Hell by his side, with her friends and family around her. Clary accepts, and asks Sebastian to put his arms around her to symbolise their unity. When he does so, she stabs him with Heosphoros. The heavenly fire turns Sebastian back into Jonathan, who expresses great remorse over what he has done as Sebastian, and guides Jace to where the Infernal Cup is hidden, beseeching him to destroy it. As soon as Jace destroys the Cup, the Endarkened fall dead.
The romantic relationships between the characters form a significant part of
City of Heavenly Fire. Alec and Magnus acknowledge the end of their relationship, but continue to have strong feelings for each other, and eventually reconcile. Jace and Clary find it difficult to be intimate while he is the vessel of the heavenly fire, as he is liable to burn her – but on the brink of the final battle with Sebastian, they have sex (the fire having left Jace and entered Heosphoros). The relationship between Simon and Isabelle develops, only to be cut short when Simon loses his immortality and his memories of the Shadow World in a deal with Magnus’ powerful father, Asmodeus, who transports Simon, the Shadowhunters and the hostages out of Edom in return. However, Simon later accepts an invitation to train as a Shadowhunter, and it appears that he and Isabelle may rekindle their relationship. In the final chapter of the novel, Jocelyn and Luke get married.