The Puritan Dilemma, The Story of John Winthrop is a brief biography of John Winthrop but also tells the story of the events that led to the Puritan colonization of America and the struggles the colonists faced in their early years. The book covers the role of Puritan theology in the Puritan relationship with the political authorities in England, its role in creating their unique culture and its role in generating one of the most democratic political bodies in the 17th century world.

The Puritans are often represented as extreme moral policemen who hate everything good in life. While the stereotype does not wholly misrepresent them, the author shows that there is much to commend in the Puritans and their first leader, John Winthrop.

The book has thirteen chapters that proceed in chronological order but are also based around important historical events. In Chapter I, the author introduces John Winthrop and discusses his childhood, early adulthood and his conversion to Christianity. It explains his education and the early recognition of his argumentative, organizational and political talents. Chapter 2 discusses how the Puritans perceive the political situation of their day under King Charles I of England. More or less, many Puritans worry whether the government was legitimate because Charles I's wife is Catholic and because Charles often persecutes Puritans.

Chapter 3 discusses the alternatives Puritans discuss for handling their current social and political condition. God's wrath, in their minds, would soon strike England due to its sins. The Puritans may very well be swept up in the punishment. With England's morality declining, the Puritans must form a "remnant" of the Godly. They eventually decide to migrate to New England to preserve their righteous religion and morality. Chapter 4 covers Puritan preparations to leave for New England and the details of how Puritan leaders secure a charter from the king to settle New England and manage to escape England with little notice.

Chapter 5 covers the migration to New England and the Puritans' first year trying to survive. Chapter 6 details the Puritans' understanding of their commission from God and how they enforce it. Chapter 7 outlines their strikingly advanced structure of government and how and why it becomes increasingly democratic. Chapter 8 covers the political and social tension the Puritans face between maintaining God's kingdom on the one hand and being reasonably lenient with the behavior of the people on the other. In Chapter 9, the author writes about the problems created by separatism and Roger Williams, whereas in Chapter 10 he discusses the challenge Anne Hutchinson brought to the colony.

Chapter 11 analyzes the Puritan form of government in detail and the debates the people have over how to structure it and which groups had which authority. The Puritans are a largely democratic people who are also very jealous of their liberties. Chapter 12 introduces the challenge presented to the Puritans by the English Civil War; since Puritans were coming to power in England, what more need would there be for preserving a remnant? Despite this concern, the Puritans stay behind. In Chapter 13, Winthrop and the people of New England face economic depression and realize that they must reach out to the wider world to find markets for their goods and services.