Now alone with Cleanthes, Philo decides to reveal what he really thinks about the whole discussion. In a surprising move, he admits to his adversary that he actually believes in the design argument. It is impossible to ignore, he concurs, the fact that everything in nature serves its purpose, that nothing is in vain, and everything is done in the simplest, best manner. These tenets guide all of our scientific reasoning, and they undeniably point to the conclusion that there is some author of this order. No one, he tells Cleanthes, can really deny this. Even atheists have to admit it (and so there is no such thing as a true atheist). The only plausible source of disagreement lies in a dispute over the extent to which God's mind is like the human mind. The theist says that God's mind is like the human mind but not too like the human mind. The atheist, on the other hand, while forced to admit that there is likely some analogy between the human mind and the first cause of the universe, does not think that this analogy is very substantive.
Philo then begs forgiveness for any impious remarks he may have made in the course of their discussion. He explains that these remarks stem from his hatred of vulgar superstitions (among which he counts all organized religion). This launches Cleanthes and Philo into a discussion about the difference between true religion (a philosophical, rational belief in some higher power), which Philo believes in fully, and organized religion, which he hates passionately.
Philo claims that organized religion is utterly destructive. First, far from promoting morality (as Cleanthes claims it does) it is actually bad for morality, as it has been responsible for so much evil in the world: it has been the cause of innumerable civil wars, persecutions, oppressions, slavery. And this is not surprising either: by focusing the believer's attention on the salvation of his own soul, it encourages selfishness rather than selflessness. The religious man is likely to care only about himself and lack a highly developed capacity to care about others.
Not only is organized religion responsible for so much bad, but also Philo does not really see how it could be effective in promoting good. Organized religion tries to influence morality with promises of reward and punishment. But men are not motivated by distant, vague, uncertain promises. They are motivated by their natural inclinations. What motivates man to be good, he is convinced, is the basic human moral sentiment of benevolence, which inclines us towards empathy and a desire for justice in the world. This natural virtue, as he calls it, is more effective than organized religion in causing us to act morally.
Not only is organized religion morally dangerous, it also causes grief, gloom, and terror in its adherents. Organized religion arises from man's terror of uncertainty but instead of making him feel joy and consolation in the face of this terror, for the most part it only makes man more terrified and more gloomy by promising that he hangs in the balance between heaven and hell.
Philo's main complaint against organized religion is that in trying to say what God is like and what God wants, organized religion oversteps its bounds. The only warranted conclusion of natural theology, he says, is this: that the cause or causes of order in the universe probably bear some remote analogy to human intelligence. Anything beyond that cannot be revealed by reason, and must remain utterly mysterious. Philo ends with a paradigmatic fideist declaration. Philosophical skepticism, he says, is the most important and fundamental step toward true Christianity, because it is only when we realize the limited capacity of reason that we turn toward revelation. And it is only revelation that shows us the true way to worship God. Empirical theism, on the other hand, can lead straight to atheism because it looks to reason to account for everything and God cannot be found in this way.