On 6 April 1632, Cotton married widow Sarah (Hawkred) Story who had a daughter.
He received word almost immediately thereafter that he was to be summoned to the High Court for his non-conforming practices.
 This was less than a year after receiving the letter from Ward.
 Cotton asked the Earl of Dorset to intercede on his behalf, but the earl wrote back that non-conformity and Puritanism were unpardonable offenses, and told Cotton "you must fly for your safety."

Cotton was to appear before William Laud, the Bishop of London, who was on a campaign to suppress Puritan practices.
He now felt that his best option was to disappear into the Puritan underground, and then decide his course of action from there.
 In October 1632, he wrote his wife a letter from hiding, saying that he was being well cared for but that she would be followed if she attempted to join him.
 Two prominent Puritans came to visit him in hiding: Thomas Goodwin and John Davenport.
 Both men came to convince him that it would be acceptable for him to conform to the established church rather than deal with possible imprisonment.
 Instead, Cotton compelled these two men into further non-conformity; Goodwin went on to be the voice of the independents (Congregationalists) at the Westminster Assembly in 1643, while Davenport became the founder of the Puritan New Haven Colony in America, using Cotton's theocratic model of government.
 It was Cotton's influence that made him "the most important of the Congregational leaders," and later a prime target for attacks by the Presbyterians.

While in hiding, Cotton moved about in an underground Puritan network, staying at times in Northamptonshire, Surrey, and different places around London.
 He contemplated going to Holland like many nonconformists, which allowed a quick return to England should the political situation become favorable and appeasing the sense that a "great reformation" was to take place soon.
 He soon ruled out Holland, however, because of the negative feedback from fellow minister Thomas Hooker who had previously gone there.

Members of the Massachusetts Bay Colony heard about Cotton's flight and sent him letters urging him to come to New England.
 None of the great Puritan clergymen had gone there, and he felt that it would put him at too great a distance to return should the situation in England warrant.
 Despite this, he made his decision to emigrate by the spring of 1633 and wrote a letter to Bishop Williams on 7 May, resigning from his benefice at St. Botolph's and thanking the bishop for his flexibility and mildness.
 By the summer, he had reunited with his wife, and the couple made their way to the coast of Kent.
 In June or July 1633, the 48 year-old Cotton boarded the ship Griffin with his wife and step-daughter, along with fellow ministers Thomas Hooker and Samuel Stone.
 Also on board was Edward Hutchinson, the oldest son of Anne Hutchinson who was traveling with his uncle Edward.
 Cotton's wife bore their son during the voyage, and they named him Seaborn.
 Eighteen months after his departure from England, Cotton wrote that his decision to emigrate was not difficult to make; he found preaching in a new land to be far preferable to "sitting in a loathsome prison."
On 6 April 1632, Cotton married widow Sarah (Hawkred) Story who had a daughter. He received word almost immediately thereafter that he was to be summoned to the High Court for his non-conforming practices.  This was less than a year after receiving the letter from Ward.  Cotton asked the Earl of Dorset to intercede on his behalf, but the earl wrote back that non-conformity and Puritanism were unpardonable offenses, and told Cotton "you must fly for your safety."
Cotton was to appear before William Laud, the Bishop of London, who was on a campaign to suppress Puritan practices. He now felt that his best option was to disappear into the Puritan underground, and then decide his course of action from there.  In October 1632, he wrote his wife a letter from hiding, saying that he was being well cared for but that she would be followed if she attempted to join him.  Two prominent Puritans came to visit him in hiding: Thomas Goodwin and John Davenport.  Both men came to convince him that it would be acceptable for him to conform to the established church rather than deal with possible imprisonment.  Instead, Cotton compelled these two men into further non-conformity; Goodwin went on to be the voice of the independents (Congregationalists) at the Westminster Assembly in 1643, while Davenport became the founder of the Puritan New Haven Colony in America, using Cotton's theocratic model of government.  It was Cotton's influence that made him "the most important of the Congregational leaders," and later a prime target for attacks by the Presbyterians.
While in hiding, Cotton moved about in an underground Puritan network, staying at times in Northamptonshire, Surrey, and different places around London.  He contemplated going to Holland like many nonconformists, which allowed a quick return to England should the political situation become favorable and appeasing the sense that a "great reformation" was to take place soon.  He soon ruled out Holland, however, because of the negative feedback from fellow minister Thomas Hooker who had previously gone there.
Members of the Massachusetts Bay Colony heard about Cotton's flight and sent him letters urging him to come to New England.  None of the great Puritan clergymen had gone there, and he felt that it would put him at too great a distance to return should the situation in England warrant.  Despite this, he made his decision to emigrate by the spring of 1633 and wrote a letter to Bishop Williams on 7 May, resigning from his benefice at St. Botolph's and thanking the bishop for his flexibility and mildness.  By the summer, he had reunited with his wife, and the couple made their way to the coast of Kent.  In June or July 1633, the 48 year-old Cotton boarded the ship Griffin with his wife and step-daughter, along with fellow ministers Thomas Hooker and Samuel Stone.  Also on board was Edward Hutchinson, the oldest son of Anne Hutchinson who was traveling with his uncle Edward.  Cotton's wife bore their son during the voyage, and they named him Seaborn.  Eighteen months after his departure from England, Cotton wrote that his decision to emigrate was not difficult to make; he found preaching in a new land to be far preferable to "sitting in a loathsome prison."
John Cotton (minister)