One of the major issues that consumed Cotton both before and after the Antinomian Controversy was the government, or polity, of the New England churches.
 By 1636, he had settled on the form of ecclesiastical organization that became "the way of the New England churches"; six years later, he gave it the name Congregationalism.
 Cotton's plan involved independent churches governed from within, as opposed to Presbyterianism with a more hierarchical polity, which had many supporters in England.
 Both systems were an effort to reform the Episcopal polity of the established Church of England.

Congregationalism became known as the "New England Way", based on a membership limited to saved believers and a separation from all other churches in matters of government.
Congregationalists wanted each church to have its own governance, but they generally opposed separation from the Church of England.
 The Puritans continued to view the Church of England as being the true church but needing reform from within.
 Cotton became the "chief helmsman" for the Massachusetts Puritans in establishing congregationalism in New England, with his qualities of piety, learning, and mildness of temper.
 Several of his books and much of his correspondence dealt with church polity, and one of his key sermons on the subject was his Sermon Deliver'd at Salem in 1636, given in the church that was forced to expel Roger Williams.
 Cotton disagreed with Williams' separatist views, and he had hoped to convince him of his errors before his banishment.
 His sermon in Salem was designed to keep the Salem church from moving further towards separation from the English church.
 He felt that the church and the state should be separate to a degree but that they should be intimately related.
 He considered the best organization for the state to be a Biblical model from the Old Testament.
 He did not see democracy as being an option for the Massachusetts government, but instead felt that a theocracy would be the best model.
It was in these matters that Roger Williams strongly disagreed with Cotton.

Puritans gained control of the English Parliament in the early 1640s, and the issue of polity for the English church was of major importance to congregations throughout England and its colonies.
 To address this issue, the Westminster Assembly was convened in 1643.
 Viscount Saye and Sele had scrapped his plans to immigrate to New England, along with other members of Parliament.
He wrote to Cotton, Hooker, and Davenport in New England, "urging them to return to England where they were needed as members of the Westminster Assembly".
 None of the three attended the meeting, where an overwhelming majority of members were Presbyterian and only a handful represented independent (congregational) interests.
 Despite the lopsided numbers, Cotton was interested in attending, though John Winthrop quoted Hooker as saying that he could not see the point of "travelling 3,000 miles to agree with three men."
 Cotton changed his mind about attending as events began to unfold leading to the First English Civil War, and he decided that he could have a greater effect on the Assembly through his writings.

The New England response to the assembly was Cotton's book The Keyes of the Kingdom of Heaven published in 1644.
It was Cotton's attempt to persuade the assembly to adopt the Congregational way of church polity in England, endorsed by English ministers Thomas Goodwin and Philip Nye.
 In it, Cotton reveals some of his thoughts on state governance. "
Democracy I do not conceive that ever God did ordain as a fit government either for church or commonwealth."
 Despite these views against democracy, congregationalism later became important in the democratization of the English colonies in North America.
This work on church polity had no effect on the view of most Presbyterians, but it did change the stance of Presbyterian John Owen who later became a leader of the independent party at the Restoration of the English monarchy in 1660.
 Owen had earlier been selected by Oliver Cromwell to be the vice-ch
One of the major issues that consumed Cotton both before and after the Antinomian Controversy was the government, or polity, of the New England churches.  By 1636, he had settled on the form of ecclesiastical organization that became "the way of the New England churches"; six years later, he gave it the name Congregationalism.  Cotton's plan involved independent churches governed from within, as opposed to Presbyterianism with a more hierarchical polity, which had many supporters in England.  Both systems were an effort to reform the Episcopal polity of the established Church of England.
Congregationalism became known as the "New England Way", based on a membership limited to saved believers and a separation from all other churches in matters of government. Congregationalists wanted each church to have its own governance, but they generally opposed separation from the Church of England.  The Puritans continued to view the Church of England as being the true church but needing reform from within.  Cotton became the "chief helmsman" for the Massachusetts Puritans in establishing congregationalism in New England, with his qualities of piety, learning, and mildness of temper.  Several of his books and much of his correspondence dealt with church polity, and one of his key sermons on the subject was his Sermon Deliver'd at Salem in 1636, given in the church that was forced to expel Roger Williams.  Cotton disagreed with Williams' separatist views, and he had hoped to convince him of his errors before his banishment.  His sermon in Salem was designed to keep the Salem church from moving further towards separation from the English church.  He felt that the church and the state should be separate to a degree but that they should be intimately related.  He considered the best organization for the state to be a Biblical model from the Old Testament.  He did not see democracy as being an option for the Massachusetts government, but instead felt that a theocracy would be the best model. It was in these matters that Roger Williams strongly disagreed with Cotton.
Puritans gained control of the English Parliament in the early 1640s, and the issue of polity for the English church was of major importance to congregations throughout England and its colonies.  To address this issue, the Westminster Assembly was convened in 1643.  Viscount Saye and Sele had scrapped his plans to immigrate to New England, along with other members of Parliament. He wrote to Cotton, Hooker, and Davenport in New England, "urging them to return to England where they were needed as members of the Westminster Assembly".  None of the three attended the meeting, where an overwhelming majority of members were Presbyterian and only a handful represented independent (congregational) interests.  Despite the lopsided numbers, Cotton was interested in attending, though John Winthrop quoted Hooker as saying that he could not see the point of "travelling 3,000 miles to agree with three men."  Cotton changed his mind about attending as events began to unfold leading to the First English Civil War, and he decided that he could have a greater effect on the Assembly through his writings.
The New England response to the assembly was Cotton's book The Keyes of the Kingdom of Heaven published in 1644. It was Cotton's attempt to persuade the assembly to adopt the Congregational way of church polity in England, endorsed by English ministers Thomas Goodwin and Philip Nye.  In it, Cotton reveals some of his thoughts on state governance. "Democracy I do not conceive that ever God did ordain as a fit government either for church or commonwealth."  Despite these views against democracy, congregationalism later became important in the democratization of the English colonies in North America. This work on church polity had no effect on the view of most Presbyterians, but it did change the stance of Presbyterian John Owen who later became a leader of the independent party at the Restoration of the English monarchy in 1660.  Owen had earlier been selected by Oliver Cromwell to be the vice-ch
John Cotton (minister)