Just as the Massachusetts Bay Colony sent Roger Williams away, an even bigger battle over religion in the colony was just around the corner. On September 18, 1634, just months before Williams was to leave the colony for good, William Hutchinson and his wife Anne Hutchinson arrived in Boston. After meeting the couple, Winthrop confided in his diary that William was "wholly guided by wife." Anne was a strong, opinionated woman, who began to believe in the Arminianism point of view after she arrived in Boston–that is, she did not believe the Puritan idea of predestination. Boston as a whole had begun to drift towards the same point of view, until its minister John Cotton firmly reasserted the Calvinist belief in 1634 and "saved" the colony.
Anne Hutchinson began to hold weekly discussion meetings in her house after joining the church, where members could talk about that week's sermon. Her beliefs tended toward the extreme ends of the spectrum, and it quickly became evident that she believed in a theory called Antinomianism–a view held as quite dangerous by the Puritans. It held that when God intervened to save someone, that person became controlled by the Holy Ghost and the person, for all intents and purposes, ceased to express free will. God need not be found in the Bible–as the Puritans taught–but could come and save a person regardless.
Hutchinson and her followers soon began to classify people as either "under a covenant of grace," (saved) or "under a covenant of works" (damned). Hutchinson gained ground quickly in the community, since as a midwife she came into contact with many members of the colony, and soon Winthrop was led to remark that dividing people between covenants of grace or works was as common as the Protestant or Catholic label in other countries. Hutchinson even hinted that all the colony's ministers except for Cotton and her brother-in-law John Wheelwright, were damned and incapable of preaching. However, she craftily never stated any of her accusations outright, and the colonial leaders had trouble deciding whether to charge her with heresy.
In October 1636, Hutchinson's supporters asked for formal recognition of their views in Cotton's Boston church and asked that Wheelwright be appointed as their spokesperson. Winthrop opposed the selection, technically appointing Wheelwright a "teacher," but Winthrop's opinions carried less weight now, and he went head- to-head against the popular new governor, Henry Vane. However, Winthrop eventually prevailed on the congregation, staging for a moment an inevitable showdown. Winthrop tried to convince the settlers to avoid Hutchinson' views in an open letter to the community–a letter his friends prevented from ever reaching the public because it alluded to Arminianism. Meanwhile, some Bostonians and the rest of the colony became increasingly concerned over Hutchinson as her followers attempted to convert more and more of the colony. The colony, however, resisted, and Governor Vane's popularity dropped as he continued to support Hutchinson. A stalemate had developed in the colony by 1637, with Boston loudly supporting Hutchinson's views, which the rest of the Massachusetts Bay Colony denounced.
Wheelwright was summoned to the General Court and convicted of sedition after he allegedly called for the murder of "damned" ministers. When he arrived later that spring to be sentenced by the court, he found that Winthrop had been reelected governor and Vane had been thrown out of the government entirely. Winthrop deferred the sentencing until the next meeting and held a mass meeting over the summer to debate the issues Hutchinson raised. He hoped that, given enough rope, Hutchinson would hang herself, which she did. At the meeting, Hutchinson's supporters rioted, bringing swift condemnation down from the rest of the colony. Her supporters began to shrink in number as her behavior turned more bizarre. Winthrop further detracted her supporters with a charitable letter explaining how wrong Hutchinson was.
Winthrop quickly put in place a new law prohibiting settlers from housing guests for more than three weeks without approval from the General Court, which prevented Hutchinson from bringing any supporters over from England.
In August, all of the ministers in Massachusetts–including Wheelwright and Cotton–and joined by a small delegation from Rhode Island, met in a synod to hash out the issues raised by Hutchinson. For twenty-four days they debated, discussed, and argued, eventually reaching a near unanimous conclusion on all counts. One by one, the synod explained almost a hundred instances of heresy and false proposals and explained in methodical detail why each was wrong. Wheelwright now stood alone against the entire assembled ministry of the new colony. Hutchinson and her ever shrinking band of followers continued to agitate for their beliefs but to no avail.
In November, the General Court banished Wheelwright and put Hutchinson on trial–which could hardly be considered a trial given that her jurors had already decided months or years before the outcome. She argued her case passionately, and the court found little with which to charge her since she so craftily phrased her sentences to avoid heresy. However, the conclusion was foregone. In a stunning conclusion, she challenged that God would punish the colony if it punished her–a view exactly counter to that held by Winthrop who believed the court and the colony stood in danger of God's wrath if they did not punish Hutchinson. The court banished her and disarmed or disenfranchised her followers. Even her church, badly split over the incident, abandoned her and voted to excommunicate her in March of 1637. She and her followers left the colony soon after. For the second time, the governor had rid itself of someone who threatened to upset the balance of the pure experiment.