2,500 years ago, the ancient Greek philosophers expressed doubts about the supernatural. However, when Christianity succeeded in taking over the Roman Empire, it also closed down the great Greek schools of philosophy and ushered in what became known as the Dark Ages. Jonathan Miller visits the absent Twin Towers to consider the religious implications of 9/11 and meets Arthur Miller and the philosopher Colin McGinn. He searches for evidence of the first 'unbelievers' in Ancient Greece and examines some of the modern theories around why people have always tended to believe in mythology and magic.

Jonathan Miller examines the religious imagery that dominated the medieval mind and investigates the role that the emerging science of men like Copernicus, Vesalius and Galileo had upon Christianity. Such was the power of the church, however, that it was not until the late 18th century in France that confident modern atheism finally emerged. With the domination of Christianity from 500 AD, he wonders how disbelief began to re-emerge in the 15th and 16th centuries. He discovers that division within the Church played a more powerful role than the scientific discoveries of the period. He also visits Paris, the home of the 18th century atheist, Baron D'Holbach, and shows how politically dangerous it was to undermine the religious faith of the masses.

Once atheism emerged, it began to challenge the moral authority of both the Church and the State. Religious doubt inspired the American War of Independence and the French Revolution, while in England the growing campaign for the rights of the working class was led by radical atheist reformers whose work helped to give birth to Socialism. The history of disbelief continues with the ideas of self-taught philosopher Thomas Paine, the revolutionary studies of geology and the evolutionary theories of Darwin. Jonathan Miller looks at the Freudian view that religion is a 'thought disorder'. He also examines his motivation behind making the series touching on the issues of death and the religious fanaticism of the 21st century.