During a conversation with Marie Webb, Alex Conklin says, "God bless, favorite lady." She responds, "He abandoned us, Alex. God doesn't exist."

This idea is repeated throughout The Bourne Ultimatum. The main character, David Webb/Jason Bourne, declares himself an agnostic. The KGB agent Dimitri Krupkin notes that he is officially atheistic, even though he sometimes calls on God. Although other characters also call on God, as Alex does when talking to Marie, the novel repeatedly emphasizes that calling on God is futile. If He exists, one character suggests, then the horrors visited on innocent lives mean that He is a "sadist." In the worlds of espionage, terrorism, and organized crime, people operate in an absence of divine justice; the people are amoral or, like Webb/ Bourne, they are lost souls searching for meaning in the unrelenting cruelty of their lives.