I think I need to drop back and read a couple books prior to this one to understand what's really going on, because there are a number of cryptic references to earlier events, but the crux of the matter is that one of Pendergast's recently-discovered twin sons, the "evil" twin, who was a serial killer in New York in an earlier story, turns up murdered on the agent's front porch one day, after a long exile in the jungles of Brazil. The agent is never one to leave a good mystery alone, and so he embarks on his own quest to find out who has killed his son, whom he despises, and why the crime was committed.
In parallel, one of Pendergast's old friends, detective d'Agosta, is involved with his own murder mystery, involving the bludgeoning death in an isolated corner of a museum, of one of the technicians who works in the department which handles old skeletons...skeletons in the closet indeed!
This one gets violent, bloody and twisty pretty quickly. I definitely have to drop back and read some of the earlier books so I get some of the major characters' back stories. Preston & Child are always good.