James Rollins' covert Sigma Force returns in his latest wild scientific thriller, Map of Bones. This time around, Painter Crowe, the protagonist of previous novels such as Sandstorm, has assumed the mantle of Sigma's leadership in the wake of revelations that the agency had been infiltrated and co-opted by the sinister Guild. He's assembled a new team of field agents, led by Grayson Pierce, a tough, independent-minded character who ended up in a military prison for a fight with a superior officer. For the record, Pierce is also quite bright, with degrees in all sorts of things (all the Sigma team members have advanced degrees and significant combat skills—it's actually hard to keep all of it straight at times).
Anyway, the novel opens with a flashback to the ancient past as a couple of monks try to keep a wagon train of relics from the hands of the evil followers of the "black pope" who had usurped control of the church. The story then cuts to present-day Germany, where a couple of young American tourists decide to join a midnight mass at the Cologne Cathedral. Unfortunately, their innocent decision means that they're caught with other parishioners when a collection of men in hooded robes invade the Cathedral, brutally kill virtually everyone present, and then steal the bones of the Three Wise Men from a gold sarcophagus (significantly, they don't bother to steal the sarcophagus itself—despite being made of gold, it isn't worth the effort).
Concerns about the way the congregation was killed (apparently, by way of "poisoned" communion wafers and some sort of electromagnetic impulse) mean that the Vatican pulls strings and gets the U.S. government to dispatch a Sigma Force team to aid local investigators in finding out what is going on. Pierce and his team join with Rachel Verona, an investigator with the carabinieri corps in Rome, and her uncle Vigor, a Catholic priest who is actually a Vatican spy. It seems that the evil Dragon Court, a medieval group of alchemists bent on world domination, still operates within the Catholic Church (and that there is likewise a "Thomas Church" which exists in tandem to the larger flow of Catholicism).
The bones of the Magi aren't really bones at all, but a highly reactive form of gold which may well have been the real-world basis of the manna from heaven which Moses and the Jews ate as they wandered in the wilderness (and which may impart certain mental abilities to those who consume it). The Dragon Court plans to use the gold to accomplish its ultimate goal, which is the unleashing of Armageddon so that they can rule the world which survives.