At the age of 7, Jesus Bar-Joseph lives with his family in Alexandria, Egypt, where they have fled to avoid a massacre of children by King Herod of Israel. Jesus knows that his parents Joseph and Mary have secrets they are keeping from him, secrets about his birth and about traits that make him very different from other boys. His parents, however, believe him too young to grasp the truth of his miraculous birth and purpose. Learning that the murderous Herod is dead, they set out to return to their home of Nazareth in Israel, unaware that Herod's namesake son is, like his father, determined to see the boy Jesus dead.

Ziad Jarrah, a young Lebonese man from a good family goes to Germany to attend college and starts dating a Turkish girl named Aysel. Although not very religious and accustomed to Western ways, Ziad becomes "brothers" with some fundamentalist Muslims and is slowly drawn into becoming "a Good Muslim". Mohamed Atta and others instill Ziad with a hatred of Jews and "Infidels", which leads to a desire for Jihad and martyrdom. He moves to Hamburg to study aeronautical engineering, attends an Al-Qaeda training camp in Afghanistan, and deceives his girlfriend and family about his involvement. He eventually attends flight school in Florida with Atta and others, waiting for and preparing for "the big wedding" (the 9/11 attack). Meanwhile, US government and law enforcement officials fail to act despite believing that a major terrorist attack is imminent, and despite noticing a number of suspicious persons involved in flight training.