Even the most bitter opponents of Roger Williams recognized in him that combination of charm, confidence and intensity a later age would call charisma. They did not regard such traits as assets, however, for those traits only made the preacher more dangerous in the Massachusetts Bay Colony. With someone like him, they could not compromise.

For his part, Williams was not about to compromise, either, despite his benevolent intelligence and Christian charity. The error, he believed, was not his, and when convinced he was right he backed away from no one.

So the conflict between Williams and his accusers nearly 400 years ago was inevitable. It was also thick with history, for it concerned both the relationship between church and state and defining the very nature of state power. Its repercussions would be immense and reach into the present.

The American part of the story began when John Winthrop led 1,000 men, women and children to plant the Massachusetts Bay Colony in 1630. These Puritans were disgusted with what they regarded as corruption in the Church of England and the tyranny of the crown. Seeking simple worship and personal intimacy with God, Puritan ministers were compelled—upon pain of imprisonment—to wear the surplice and use the Book of Common Prayer, and their congregants were compelled to participate in what they regarded as rote worship. As they set out from England that April, Winthrop reminded them of their purpose, to establish a “citty upon a hill” dedicated to God, obeying God’s laws and flourishing in God’s image as a model for all the world to see.

Williams, who had developed a reputation for scholarship and piety as a clergyman in England, brought his family to the colony a few months later. Winthrop hailed him as “a godly minister,” and the Boston church immediately offered him a post, the greatest such position in English America. But Williams declined, spurning the church as insufficiently committed to the proper wors...