Among the members of Cotton’s church was Mrs. Anne Hutchinson, who knew Cotton in England and had crossed the sea to hear his teachings.  After her arrival, in June, 1636, she made herself very popular by her ministrations “in time of childbirth and other occasions of bodily infirmities.”  Soon she ventured to hold open meetings for women, at which the sermons of the ministers furnished the subject of comment.  From a mere critic of the opinions of others Mrs. Hutchinson gradually presumed to act the part of teacher herself, and her views on the questions of “a covenant of works” and “a covenant of grace” attracted much attention.[10] The former of these terms had been used by Protestants to designate the condition of the Catholic church, which imposed as the condition of salvation penances, confessions, pilgrimages, legacies to the church, etc.; while the latter expression described the condition of all true Protestant Christians who found peace in the consciousness of holiness of spirit and faith in Jesus Christ.

Mrs. Hutchinson gave an emotional rendering to the “covenant of grace,” and held that the divine spirit dwelt in every true believer and no demeanor in life could evidence its existence.  To the Massachusetts ministers this doctrine seemed like a claim to inspiration, and struck at the whole discipline of the church.  But what disturbed them more than anything else was the report that she had singled out two of the whole order, John Cotton and her brother-in-law John Wheelwright, to praise as walking in “the covenant of grace."[11]

The quarrel began first in the bosom of the Boston church.  Wilson, the pastor, resented Mrs. Hutchinson’s preference of Mr. Cotton, the teacher, and began to denounce Mrs. Hutchinson’s opinions.  The congregation divided into two factions; on the one side was the pastor, supported by John Winthrop and a few others, and on the other were Mrs. Hutchinson, young Harry Vane, then governor, and the large majority of the members.  Mr. Cotton was not identified with either side, but sympathized with the latter.  Matters verged to a crisis when the Hutchinsonians announced their intention of electing Mr. Wheelwright, who had not long since arrived, as a second teacher in the church.

The election was to take place on Sunday, October 30, 1636; but October 25 the general court met and the ministers from other parts of the colony came to Boston and held a conference at which Cotton, Wheelwright, and Wilson were present, and there was a general discussion of all points in controversy.  They agreed that “sanctification” (i.e., a holy deportment) did help to evidence “justification” (salvation); but there was more or less difference on the question of the “indwelling of the Holy Ghost.”  Mr. Wheelwright argued in its favor, but held that the indwelling referred to did not amount to “a personal union with God,” as Mrs. Hutchinson and Governor Vane contended.