City of Bones is set in long-post-apocalypse Charisat, where the city's eight levels divide the haves from the have-nots and water instead of gold is the currency by which most trade is conducted. Khat, a young krismen (a minority race created through genetic modification by the scientist-magicians of the Ancients - the technologically sophisticated, pre-apocalypse culture), is a skilled relic hunter who draws the unwanted attention of the city's Warders - magically-trained protectors of the ruler. When the Master Warder's protege, Elen, seeks out Khat to act as her guide to one of the Remnants - mysterious towers scattered around Charisat - neither of them realize they are about to become involved not only in political intrigue at the highest levels, but also in unraveling some of the most puzzling questions about the Ancients: What was the purpose of the Remnants? What is the Miracle, the large, unexplained artifact housed on the elite First Tier, home of the Elector and the Warders, which sat inert in the Elector's garden until it began emitting flashes of light 20 years prior? Why did the Ancients create the Krismen? And why does use of their magic drive some Warders insane?
Khat's genetic heritage, innate intelligence, and knowledge of historical artifacts all serve both to place him in harm's way and also get him out of trouble.