In October 1636, Governor Winthrop noted in his journal that Hutchinson had become the cause of a debate over certain points of theology, and listed several "errors" promulgated by Hutchinson, adding that "there joined with her in these opinions a brother of hers, one Mr. Wheelwright, a silenced minister sometimes in England." During the same month, the ministers confronted the issue, and gathered for a "private conference" with Cotton, Mrs. Hutchinson, and Wheelwright, who was actually her husband's brother-in-law, who had just arrived in the colony. In this meeting, agreement was reached, and Cotton "gave satisfaction to them [the other ministers], so as he agreed with them all in the point of sanctification, and so did Mr. Wheelwright; so as they all did hold, that sanctification did help to evidence justification." This, however, did not quell the differences of opinion in the Boston church, and a majority of the members were of the opinion of Hutchinson, and proposed that Wheelwright join the church ministry. This was an attempt to replace the church's minister, John Wilson, who was a personal friend of Winthrop. Winthrop, taking advantage of a rule requiring unanimity in a church vote, was able to thwart Wheelwright's election, and had him sent to another church at Braintree, ten miles away. The ministers then met again in December, and drew up a list of 16 points wherein they suspected that Cotton disagreed with the others, and Cotton was pressed for direct answers, yay or nay, to each point. In general, they were not trying to overwhelm Cotton with theological arguments, but wanted to alert him to the "dangerous conclusions others were drawing from his position." Additionally, they were trying to vindicate their reputations as orthodox Protestants who still believed in "free grace."
By late 1636, as the controversy came to a boil, Hutchinson and her followers were accused of two heresies in the Puritan church: antinomianism and familism. The word "antinomianism" literally means "against or opposed to the law;" in a theological context it means "the moral law is not binding upon Christians, who are under the law of grace." Technically, if one was under the law of grace then moral law did not apply, raising the specter of a range of deviant behavior in the eyes of the church and society. Familism was named for a 16th century sect called the Family of Love, and Hutchinson and her followers were incorrectly accused of engaging in "free love," a label that was actually antithetical to their beliefs.
The colonists who embraced the law of grace did not call themselves Antinomians, since to them the term implied licentious behavior and religious heterodoxy. The term was used, instead, by the opponents of the "Antinomians" to discredit them. The controversy boiled down to a struggle for control of Massachusetts; it came at a time when the new society was forming, and it had a decisive effect upon the future of New England. While Hutchinson took a leading role as the chief antagonist of the orthodox party, it was actually John Cotton's differences of opinion with the other ministers in Massachusetts that was at the heart of the controversy. The controversy took place over a period of about 17 months, from October 1636 to the time of Hutchinson's church trial in March 1638.
Ultimately, Hutchinson was brought to civil trial by the General Court in November 1637, presided over by Governor John Winthrop, on the charge of “traducing the ministers.” The Court included both government officials and Puritan clergy. She was 46 at the time and apparently advanced in pregnancy. Nevertheless, she was forced to stand for many hours for two days before a board of male interrogators as they tried desperately to get her to admit her secret blasphemies. They accused her of violating the fifth commandment–to "honor thy father and mother"–accusing her of encouraging dissent against the fathers of the commonwealth. It was charged that by attending her gatherings women were being tempted to neglect the care of their own families.
At the end of the first day of the trial, as the hour grew late, Winthrop recorded, "Mrs. Hutchinson, the court you see hath labored to bring you to acknowledge the error of your way that so you might be reduced. The time now grows late. We shall therefore give you a little more time to consider of it and therefore desire that you attend the court again in the morning." The first day had gone well for the prisoner, as Winthrop referred to Hutchinson; she had outfenced the magistrates in a battle of wits and forced the ministers into publicly revealing a private and confidential conversation. As LaPlante wrote, "Her success before the court may have astonished her judges, but it was no surprise to her. She was confident of herself and her intellectual tools, largely because of the intimacy she felt with God..."
The defense's star witness was Cotton, who was as much on trial as Hutchinson. Were he to refute the accusations of his fellow ministers, he would have earned their lasting enmity; but should he repudiate Hutchinson's advocacy and devotion, he would destroy his reputation for loyalty and integrity. Using courage and tact, Cotton was able to deflect the magistrate's questions, or not remember certain things that Hutchinson supposedly said. Cotton, in a soft and conciliatory tone, seriously modified the black-and-white version of the conference that the other elders insisted upon, putting the Governor and other magistrates in a very awkward position.
Fearful that Hutchinson's example might be imitated by other women, the divines wished to catch her in a major theological error, then subject her to public punishment. They were not immediately successful, as she was able to parry their verbal thrusts by replying to their many questions with questions of her own, forcing them to justify their positions from the Bible, and then pointing out their inconsistencies. With crucial assistance from a sympathetic Cotton, she left the ministers with no charge to pin on her.
As the trial progressed during the second day, it became apparent where the proceedings were going. Hutchinson defended herself until it was clear that there was no escape from the court’s predetermined judgment. Impulsively, she took the load off the consciences of her accusers, and asked the court for leave to "give you the ground of what I know to be true." Cornered, she addressed the court with her own judgment:
You have no power over my body, neither can you do me any harm—for I am in the hands of the eternal Jehovah, my Saviour, I am at his appointment, the bounds of my habitation are cast in heaven, no further do I esteem of any mortal man than creatures in his hand, I fear none but the great Jehovah, which hath foretold me of these things, and I do verily believe that he will deliver me out of our hands. Therefore take heed how you proceed against me—for I know that, for this you go about to do to me, God will ruin you and your posterity and this whole state.
— Anne Hutchinson at trial
Those in the courtroom were stunned; no man in the colony had ever gone as far as invoking a curse upon the elders of the New Zion, and here it was being done by a woman. After the silence, her outburst brought forth jeers. The magistrates had heard all they needed and were ready to begin sentencing, when William Coddington rose to make a last effort on behalf of the prisoner, saying, "I do not see any clear witness against her, and you know it is a rule of the court that no man may be a judge and an accuser too. I would entreat you to consider whether those things which you have alleged against her deserve such censure as you are about to pass, be it to banishment or imprisonment. I beseech you: do not speak so as to force things along, for I do not, for my own part, see any equity in the court in all your proceedings. Here is no law of God that she hath broken nor any law of the country that she hath broke, and therefore deserve no censure."
Coddington was ignored. Hutchinson was called a heretic and an instrument of the devil. In the words of one minister, "You have stepped out of your place, you have rather been a husband than a wife, a preacher than a hearer, and a magistrate than a subject." In late 1637 she was condemned to banishment by the Court "as being a woman not fit for our society". She was put under house arrest to await her religious trial.
Thus ended the civil trial of Hutchinson, in an infant community whose leaders looked on democracy as the worst form of government. The Puritans sincerely believed that in banishing Hutchinson they were protecting God's eternal truth. Winthrop summed up the case with genuine feeling: "Thus it pleased the Lord to heare the prayers of his afflicted people...and by the care and indevour of the wise and faithfull ministers of the Churches, assisted by the Civill authority, to discover this Master-piece of the old Serpent, and to break the brood by scattering the Leaders, under whose conduct hee had prepared such Ambushment, as in all reason would soon have driven Christ and Gospel out of New England, (though to the ruine of the instruments themselves, as well as others) and to the repossessing of Satan in his ancient Kingdom; It is the Lords work, and it is marvellous in our eyes."
Following her civil trial, Hutchinson would not be released until she underwent a trial by the clergy, and this would not take place until the following March. In the interim, she was not allowed to return home, but instead was detained at the house of Joseph Weld, brother of the Reverend Thomas Weld, which was located in Roxbury, about two miles from her home in Boston. While the distance was not great, Hutchinson was rarely able to see her children because of the winter weather, which was particularly harsh that year. Winthrop, who referred to Hutchinson as "the prisoner," was determined to keep her isolated so that others would not be inspired by her. She was frequently visited by the various preachers, whose intent was to reform her thinking, and also to collect evidence against her for use in her church trial set for early spring.
When asked, during her civil trial, how she knew that "God will ruine you and your posterity..." she answered "By an immediate revelation," thus proving her heresy to the ministers, leading to excommunication proceedings conducted before the Boston church in March 1638. They accused Hutchinson of blasphemy. They also accused her of "lewd and lascivious conduct" for having men and women in her house at the same time during her Sunday meetings. On 22 March, this religious court found her guilty and voted to excommunicate her from the Puritan Church for dissenting from Puritan orthodoxy.
Cotton, "smarting from a psychological slap Anne had given him earlier in the exommunication proceedings and in danger of losing the respect of the other ministers," had now turned against her and admonished her with these words, "though I have not herd, nayther do I thinke, you have bine unfaythfull to your Husband in his Marriage Covenant, yet that will follow upon it." He finished his admonition, criticizing her pride in saying, "I have often feared the highth of your Spirit and being puft up with your owne parts." By suggesting that Hutchinson supported promiscuity (though far from her intentions), the congregation was distanced from supporting her. Cotton warned the Boston women that Hutchinson was "but a Woman and many unsound and dayngerous principles are held by her." The Reverend Thomas Shepard warned that intellectual activity did not suit women, and that she was likely to "seduce and draw away many, Espetially simple Weomen..." Five supporters of Hutchinson, including Thomas Oliver and her brother-in-law, Richard Scott, were dismissed from the proceedings by Cotton as being either self-interested parties, or having a natural affection for her. Hutchinson was banished, and her leading supporters, including Coddington and John Coggeshall, were given three months to leave the colony, while others were disenfranchised. The court ordered that 58 citizens of Boston and 17 from adjacent towns be disarmed unless they repudiated the "seditious label" given them.
During Hutchinson's imprisonment, several of her supporters prepared to leave the colony and settle elsewhere. A group of her followers, including her husband Will, met on 7 March 1638, at the home of the wealthy Boston merchant William Coddington. Ultimately 23 men signed what is known as the Portsmouth Compact, forming themselves into a "Bodie Politick" and electing Coddington as their governor, but giving him the Biblical title of "judge." Of the signers, 19 of them initially planned to move to New Jersey or Long Island, but Roger Williams convinced them to settle in the area of his Providence Plantations settlement. Coddington purchased Aquidneck Island, in the Narragansett Bay, from the Narragansetts and the settlement of Pocasset (soon renamed Portsmouth) was founded. Anne Hutchinson followed in April, after the conclusion of her church trial.
Hutchinson, her children, and others accompanying her traveled for more than six days by foot in the April snow to get from Boston to Roger Williams' settlement at Providence. They then took boats to get to Aquidneck Island, where many men had gone ahead of them to begin constructing houses. In the second week of April, she reunited with her husband, from whom she had been separated for nearly six months.