Cotton had been deeply complicit in the controversy because his theological views differed from those of the other ministers in New England, and he suffered in attempting to remain supportive of Hutchinson while being conciliatory towards his fellow ministers.
 Nevertheless, some of his followers were taking his singular doctrine and carrying it well beyond Puritan orthodoxy.
 Cotton attempted to downplay the appearance of colonial discord when communicating with his brethren in England.
A group of colonists made a return trip to England in February 1637, and Cotton asked them to report that the controversy was about magnifying the grace of God, one party focused on grace within man, the other on grace toward man, and that New England was still a good place for new colonists.

Cotton later summarized some of the events in his correspondence.
 In one letter he asserted that "the radical voices consciously sheltered themselves" behind his reputation.
 In a March 1638 letter to Samuel Stone at Hartford, he referred to Hutchinson and others as being those who "would have corrupted and destroyed Faith and Religion had not they bene timely discovered."
 His most complete statement on the subject appeared in a long letter to Wheelwright in April 1640, in which he reviewed the failings which both of them had committed as the controversy developed.
 He discussed his own failure in not understanding the extent to which members of his congregation knowingly went beyond his religious views, specifically mentioning the heterodox opinions of William Aspinwall and John Coggeshall.
 He also suggested that Wheelwright should have picked up on the gist of what Hutchinson and Coggeshall were saying.

During the heat of the controversy, Cotton considered moving to New Haven, but he first recognized at the August 1637 synod that some of his parishioners were harboring unorthodox opinions, and that the other ministers may have been correct in their views about his followers.
 Some of the magistrates and church elders let him know in private that his departure from Boston would be most unwelcome, and he decided to stay in Boston once he saw a way to reconcile with his fellow ministers.

In the aftermath of the controversy, Cotton continued a dialogue with some of those who had gone to Aquidneck Island (called Rhode Island at the time).
 One of these correspondents was his friend from Lincolnshire William Coddington.
 Coddington wrote that he and his wife had heard that Cotton's preaching had changed dramatically since the controversy ended: "if we had not knowne what he had holden forth before we knew not how to understand him."
 Coddington then deflected Cotton's suggestions that he reform some of his own ideas and "errors in judgment".
 In 1640, the Boston church sent some messengers to Aquidneck, but they were poorly received.
 Young Francis Hutchinson, a son of Anne, attempted to withdraw his membership from the Boston church, but his request was denied by Cotton.

Cotton continued to be interested in helping Wheelwright get his order of banishment lifted.
 In the spring of 1640, he wrote to Wheelwright with details about how he should frame a letter to the General Court.
 Wheelwright was not yet ready to concede the level of fault that Cotton suggested, though, and another four years transpired before he could admit enough wrongdoing for the court to lift his banishment.

Some of Cotton's harshest critics during the controversy were able to reconcile with him following the event.
 A year after Hutchinson's excommunication, Thomas Dudley requested Cotton's assistance with counseling William Denison, a layman in the Roxbury church.
 In 1646, Thomas Shepard was working on his book about the Sabbath Theses Sabbaticae and he asked for Cotton's opinion.
Cotton had been deeply complicit in the controversy because his theological views differed from those of the other ministers in New England, and he suffered in attempting to remain supportive of Hutchinson while being conciliatory towards his fellow ministers.  Nevertheless, some of his followers were taking his singular doctrine and carrying it well beyond Puritan orthodoxy.  Cotton attempted to downplay the appearance of colonial discord when communicating with his brethren in England. A group of colonists made a return trip to England in February 1637, and Cotton asked them to report that the controversy was about magnifying the grace of God, one party focused on grace within man, the other on grace toward man, and that New England was still a good place for new colonists.
Cotton later summarized some of the events in his correspondence.  In one letter he asserted that "the radical voices consciously sheltered themselves" behind his reputation.  In a March 1638 letter to Samuel Stone at Hartford, he referred to Hutchinson and others as being those who "would have corrupted and destroyed Faith and Religion had not they bene timely discovered."  His most complete statement on the subject appeared in a long letter to Wheelwright in April 1640, in which he reviewed the failings which both of them had committed as the controversy developed.  He discussed his own failure in not understanding the extent to which members of his congregation knowingly went beyond his religious views, specifically mentioning the heterodox opinions of William Aspinwall and John Coggeshall.  He also suggested that Wheelwright should have picked up on the gist of what Hutchinson and Coggeshall were saying.
During the heat of the controversy, Cotton considered moving to New Haven, but he first recognized at the August 1637 synod that some of his parishioners were harboring unorthodox opinions, and that the other ministers may have been correct in their views about his followers.  Some of the magistrates and church elders let him know in private that his departure from Boston would be most unwelcome, and he decided to stay in Boston once he saw a way to reconcile with his fellow ministers.
In the aftermath of the controversy, Cotton continued a dialogue with some of those who had gone to Aquidneck Island (called Rhode Island at the time).  One of these correspondents was his friend from Lincolnshire William Coddington.  Coddington wrote that he and his wife had heard that Cotton's preaching had changed dramatically since the controversy ended: "if we had not knowne what he had holden forth before we knew not how to understand him."  Coddington then deflected Cotton's suggestions that he reform some of his own ideas and "errors in judgment".  In 1640, the Boston church sent some messengers to Aquidneck, but they were poorly received.  Young Francis Hutchinson, a son of Anne, attempted to withdraw his membership from the Boston church, but his request was denied by Cotton.
Cotton continued to be interested in helping Wheelwright get his order of banishment lifted.  In the spring of 1640, he wrote to Wheelwright with details about how he should frame a letter to the General Court.  Wheelwright was not yet ready to concede the level of fault that Cotton suggested, though, and another four years transpired before he could admit enough wrongdoing for the court to lift his banishment.
Some of Cotton's harshest critics during the controversy were able to reconcile with him following the event.  A year after Hutchinson's excommunication, Thomas Dudley requested Cotton's assistance with counseling William Denison, a layman in the Roxbury church.  In 1646, Thomas Shepard was working on his book about the Sabbath Theses Sabbaticae and he asked for Cotton's opinion.
John Cotton (minister)