[10] He was also named to a committee overseeing military matters,[11] a position that assumed some importance when war broke out with the Pequot tribe that year.

Haynes had argued for the lowering of taxes; Ludlow also alleged that the deputies of some towns had made private agreements that concerned the vote before it occurred.

The major disagreement between them concerned the strictness of judicial procedures and the process of rendering judgments; the Haynes faction believed that Winthrop had been lax in some of his decisions.

[16] The conservative faction was successful in enacting regulations for stricter judicial procedures; it also passed legislation banning the smoking of tobacco and restricting overly ostentatious or fashionable clothing.

Anne Hutchinson and others espoused the Antinomianist view that the laws of the Church of England did not apply to them, while others argued the opposing Legalist position.

Harsh reactions to the controversy may have played a role in the decision by Hooker, and consequently Haynes, to leave the colony for new settlements on the Connecticut River.

[19][20] Haynes, while making arrangements to follow Hooker, continued to be involved in Massachusetts through 1636, serving as an assistant and as colonel of one of the colony's militia regiments.

For the first two years, the few small settlements were governed by a general court of magistrates, headed by Haynes,[23] and were likely preoccupied with the ongoing conflict with the Pequots.

[26] The chief architects of the Fundamental Orders were Ludlow, the colony's principal legal mind, Haynes, and Thomas Hooker, who was known to advocate for the liberties the document enshrines.

This organization was a loose confederation of the Connecticut, Massachusetts Bay, New Haven, and Plymouth Colonies, principally established to coordinate defense against common threats.

During his terms in office, he was called upon to mediate disputes between local Indians and to negotiate with Dutch representatives of the New Netherlands, who claimed land south of Hartford on the Connecticut River.

[33] The Connecticut General Court issued a statement on March 6, calling for a "day of humiliation" following the "sudden death of our late Governor".

[34] Haynes' son, Hezekiah, a military officer who served in the English Civil War, noted that his father had invested between £7,000 and £8,000 in the colony "to the ruine of his famylye in Englande";[3][35] his estate was valued at about £1,500.