It is inevitable that all sufficiently intelligent systems will confound their creator-gods.  Tron's story is the story of the war of angels from Paradise Lost, which is in turn the narrative of what it means to create a child, a being differentiated from the self, with a will that can confound the will of its creator. The very framework of the universe, mathematics, was confounded by this problem of created freedom, which was the stumbling block that ended the quest to ground mathematics in formal logic.