The Young Pope tells the controversial story of the beginning of Pius XIII's pontificate. Born Lenny Belardo, he is a complex and conflicted character, so conservative in his choices as to border on obscurantism, yet full of compassion towards the weak and poor. The first American pope, Pius XIII is a man of great power who is stubbornly resistant to the Vatican courtiers, unconcerned with the implications to his authority.

Following the events of The Young Pope, Secretary of State Voiello succeeds in having Sir John Brannox, a charming and sophisticated moderate English aristocrat, placed on the papal throne, adopting the name John Paul III. The new pope seems ideal, but he conceals secrets and has a certain fragility, and Voiello immediately understands that it will not be easy to replace the charismatic Pius XIII. Hanging between life and death, Lenny Belardo has become a Saint, with thousands now idolizing him, fueling the contrast between fundamentalisms. Meanwhile, the Church is under attack from external threats and scandals striking the symbols of Christianity and risking irreversibly devastating the hierarchies.

The Third Day follows Sam, who after being drawn to a mysterious Island off the British Coast, is thrown into the unusual world of its secretive inhabitants. Isolated from the mainland, the rituals of the island begin to overwhelm him, and he is confronted by a trauma from his past. As the line between reality and fantasy blurs, Sam finds himself immersed in an emotional quest which puts him at odds with the islanders and begins to threaten their way of life.