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.