After Father Giulio Azetti, a priest in the remote Italian village of Montecastello, hears a shocking confession from the elderly Dr. Ignazio Baresi he rushes to the Vatican to inform the Church leadership. The secret of the confession was meant to only be shared with Cardinal Orsini, the head of the Congregation for the Doctrine of the Faith, but is overheard by the Cardinal's temporary secretary Father Donato Maggio, a member of the right-wing reactionary Catholic group Umbra Domini ("The Shadow of the Lord"). While the Church officially decides to put the matter of Baresi's confession on hold, Maggio passes on the news to the leader of Umbra Domini, Father Silvio della Torre, who states that "there is only one thing that can be done".
In a wealthy suburb of Washington, D.C. a house suddenly explodes in flames, throwing a man violently into the grass and killing Kathy Lassitter and her young son Brandon who lived inside. Kathy's brother, private investigator Joe Lassiter, works to uncover the identity of the "John Doe" found outside his sister's house (now recovering in hospital) as well as the reason Kathy and her son were killed.
Contains examples of:
- Church Militant: Franco Grimaldi, aka "John Doe", a former mercenary assassin turned Umbra Domini assassin
- Umbra Domini calls for "a more muscular Catholicism", with some characters comparing them to a Catholic version of Hamas
- Clone Jesus: The goal of Baresi's work by extracting cells from holy relics considered to be most likely to be genuine parts of Jesus' body and implanting them in women seeking to become pregnant
- Jesse, the only child created by Baresi's procedure to survive, is firmly implied to be this when he brings a dead fish back to life in the Epilogue
- Dark Is Evil: Umbra Domini, often shortened by many characters to simply Umbra ("Shadow")
- Dead Man Writing: Baresi's letter to Father Azetti, spelling out the reasoning behind what he did
- Funetik Aksent: Tommy Truong, the medical examiner friend of Joe's that autopsies Kathy and BrandonTruong: "Oh, Cho. Very sorry. So very sorry."
- Foreshadowing: One of the officer's supervising Grimaldi's transfer from the hospital remarks on the attractiveness of the nurse but remembers hearing the other nurses say she was "some kind of religious nut"
- Fictional Counterpart: Umbra Domini is a fictionalized version of the conspiracies/controversies that surrounded the actual Catholic organization Opus Dei
- Hospital Hottie: Juliette, the nurse who helps Grimaldi escape is remarked to be this by one of the cops
- Info Dump: Everything from the bureaucracy of the Catholic Church to fertility procedures.
- Kill It with Fire: Umbra Domini's response to the 18 children that may potentially be genetic offspring of Jesus
- Justified in that the bodies needed to be thoroughly burned to ash in order to remove any genetic material that could be extracted.
- Minor Crime Reveals Major Plot: Starts with the relatively minor crime of the killing of Joe Lassiter's sister and nephew, and ends with the reveal of a major conspiracy to murder children conceived by a new fertility procedure using genetic material of Jesus obtained from holy relics
- The Mole: Umbra Domini has several.
- Father Maggio, Cardinal Orsini's secretary.
- Juliette, the nurse that helps Grimaldi escape the hospital and fake a carjacking
- Tom Drabowski, the FBI Agent brought in to "investigate" the carjacking that helps Grimaldi escape police surveillance
- Private Investigator: Joe Lassiter and his company, Lassiter Associates.
- Renaissance Man: Baresi was a genius in genetics, theology (specifically religious relics), and fertility
- Those Two Guys: Nigel and Hugh, the gay couple that run the pensione in Montecastello
- Villain with Good Publicity: Umbra Domini has a slick and efficient PR machine, with Father della Torre himself described as being "movie star" handsome and very media-savvy
- Would Hurt a Child: Umbra Domini has 17 of the children born from Baresi's procedure (and their mothers) murdered, and they almost kill the 18th.