In the third episode of the series, Morgan Freeman examines different faiths' concepts of God, discovering how monotheism began in Egypt and Israel and allowing a neuroscientist to examine his own brain.

Atheist and scientist Richard Dawkins visits England, America and Israel interveiwing prominant people of faith; Islamic, Hasidic Jews, and the new Christian sects popping up throughout the world, and expressing his view of the extent to which this fanaticism has degraded our civilisation, and will continue to degrade it. "The God Delusion" explores the unproven beliefs that are treated as factual by many religions and the extremes to which some followers have taken them. Dawkins opens the programme by describing the "would-be murderers ... who want to kill you and me, and themselves, because they're motivated by what they think is the highest ideal." Dawkins argues that "the process of non-thinking called faith" is not a way of understanding the world, but instead stands in fundamental opposition to modern science and the scientific method, and is divisive and dangerous.

In the last episode of the series, Freeman examines different faiths' views on miracles, meeting a man who survived falling 47 storeys and a cancer patient who believes his illness can be cured by prayer.

In the fourth episode, Morgan Freeman examines how different faiths see the creation of the world, taking him on a journey to the Vatican, Cairo and the jungles of Guatemala.

Over one billion Christians look to Rome, more than half of all Christians on the planet. But how did a small Jewish sect from the backwoods of 1st-century Palestine, which preached humility and the virtue of poverty, become the established religion of western Europe - wealthy, powerful and expecting unfailing obedience from the faithful? Amongst the surprising revelations, Professor MacCulloch tells how confession was invented by monks on a remote island off the coast of Ireland, and how the Crusades gave Britain the university system. Above all, it is a story of what can be achieved when you have friends in high places.

In the fourth part of the series, Diarmaid MacCulloch makes sense of the Reformation, and of how a faith based on obedience and authority gave birth to one based on individual conscience. He shows how Martin Luther wrote hymns to teach people the message of the Bible, and how a tasty sausage became the rallying cry for Swiss Reformer Ulrich Zwingli to tear down statues of saints, allow married clergy and deny that communion bread and wine were the body and blood of Christ.