While Daybreak marks the initiation of the project of re-evaluation, Nietzsche's work in The Gay Science and in Beyond Good and Evil represents a process of development and revision in his understanding of the nature of this task. Specifically, Nietzsche gradually identifies three major problems:

• His analysis in Daybreak had presupposed that the loss of belief in God would lead directly to a loss of authority of Christian moral beliefs; although people would still act as if this morality were authoritative in that they would still, at least for a time, be characterized by the moral sentiments cultivated by Christianity, they would no longer accept the authority of the moral beliefs characteristic of Christianity. However, Nietzsche comes to see this assumption as problematic. By the time of composing Book III of The Gay Science it appears to him that his contemporaries, while increasingly characterized by atheism, do not understand this loss of faith to undermine the authority of Christian morality. It is not that they act in accordance with morality while no longer believing in it, but that they still believe in morality, that is, they take the authority of Christian morality to be unaffected by the fact that they no longer believe in God.

• In Daybreak, Nietzsche had taken the authority of scientific knowledge for granted in making his case. However, he comes to acknowledge that this cannot simply be assumed given the constraint of naturalism that characterizes his project and given that he requires a naturalistic account of how we come to value truth and why this should lead us to reject Christian morality.

• With the exception of his remarks on suffering, the account in Daybreak had failed to provide any compelling basis for reevaluating moral values that did not simply express Nietzsche’s own evaluative commitments. Nietzsche comes to see this problem as related to the inadequacy of his account of how we come to be committed to Christian morality at all since, as he will later stress in Beyond Good and Evil, the establishment of Christianity promised “a revaluation of all the values of antiquity” (BGE §46).