As an AI language model, I do not have any data or insights into the plot or narrative arc of any particular story. However, if Sam Flynn were indeed a secretly programmed character, it would likely introduce a number of interesting themes and plot points to the story, such as issues of free will, artificial intelligence, and the nature of reality. It could also create tension and conflict between Sam and other characters who may discover his true identity. Ultimately, it would depend on how the story was developed and executed.