But the new patent did not bring peace to the colony. In 1649, Roger Williams wrote to Governor Winthrop: "Our poor colony is in civil dissension. Their last meeting [of the assembly] at which I have not been, have fallen into factions. Mr. Coddington and Captain Partridge, etc., are the heads of one, and Captain Clarke, Mr. Easton, etc., the heads of the other." What had happened was this. Coddington, representing the conservative and theocratic wing of the assembly and opposing those who were more liberally minded, had evidently applied to Massachusetts and Plymouth for support in the effort to obtain an independent government for Aquidneck. This plan would have destroyed what unity the colony had obtained under the patent, but Coddington wished to be governor of a colony of his own. Both Massachusetts and Plymouth were favorable to this plan, as they hoped to further their own claims to the territory of islands and mainland. Twice Coddington made application to the newly formed Confederation of New England for admission, but was refused unless he would bring in Aquidneck as part of Massachusetts or Plymouth, the latter of which laid claim to it. Coddington himself was willing to do this but found the opposition to the plan so vehement that he gave up the attempt and went to England to secure a patent of his own. After long negotiations he was successful in his quest and returned with a document which appointed him governor for life with almost viceregal powers. But he had reckoned without the people whom he was to govern. Learning of the outcome of Coddington's mission and hearing that he had had secret dealings also with the Dutch at New Amsterdam, the inhabitants of the islands rose in revolt, hanged Captain Partridge and compelled Coddington to seek safety in flight. Williams again went to England in 1651 and procured the recall of Coddington's commission and a confirmation of his own patent, and Coddington in 1656 gave in his submission and was forgiven, The early history of Rhode Island thus furnishes a remarkable exhibition of intense individualism in things religious and a warring of disruptive forces in matters of civil organization.

Connecticut was settled during the years 1634 to 1636 by people from Massachusetts. Knowledge of the fertile Connecticut valley had come early to the Dutch, who had planted a blockhouse, the House of Good Hope, at the southeast corner of the land upon which Hartford now stands. Plymouth, too, in searching for advantageous trade openings had sent out one William Holmes, who sailed past the Dutch fort and took possession of the site of Windsor. In the autumn of 1634 a certain John Oldham, trader and rover and frequent disturber of the Puritan peace, came with a few companions and began to occupy and cultivate lands within the bounds of modern Wethersfield. Settlers continued to arrive from Massachusetts, either by land or by water, actuated by land-hunger and stirred to movement westward by the same driving impulse that for years to come was to populate the frontier wherever it stretched. The territory thus possessed was claimed at first by Massachusetts, on the theory that the southern line of the colony, if extended westward, would include this portion of the Connecticut River. It was also claimed by the group of English lords and gentlemen, Saye and Sele, Brooke, and other Puritans, who, as they supposed, had obtained through the Earl of Warwick from the New England Council a grant of land extending west and southwest from Narragansett Bay forty leagues. These claims were of course irreconcilable, but the English lords, in order to assert their title, sent over in 1635 twenty servants, known as the Stiles party, who reached Connecticut in the summer of that year. Thus by autumn there were on the ground four sets of rival claimants: the Dutch, the Plymouth traders, various emigrants from Massachusetts, chiefly from the town of Dorchester, and the Stiles party, representing the English lords and gentlemen. Their relations were not harmonious, for the Dutch tried to drive out the Plymouth traders, and the latter resented in their turn the attempt of the Dorchester men to occupy their lands.

The matter was to be settled not by force but by weight of numbers and soundness of title. In 1635, a new and larger migration was under consideration in Massachusetts, prompted by various motives: partly personal, as shown in the rivalries of strong men in a colony already overstocked with leaders; partly material, as indicated by the desire for wider fields for cultivation and especially good pasture; and partly political, as evidenced by the dislike on the part of many for the power of the elders and magistrates in Massachusetts and by the strong inclination of masterful men toward a government of their own. Thomas Hooker, the pastor of the Newtown church, John Haynes, the Governor of Massachusetts in 1635, and Roger Ludlow, a former magistrate and deputy governor who had failed of election to the magistracy in the same year, were the leaders of the movement and, if we may judge from later events, were believers in certain political ideas that were not finding application in the Bay Colony. Disappointed because of the rigidity of the Massachusetts system, they seem to have waited for an opportunity to put into practice the principles which they believed essential to the true government of a people.

When the decision was finally reached and certain of the inhabitants of Newtown, Watertown, and Roxbury were ready to enter on their removal, the question naturally arose as to the title to the territory. In June, 1635, Massachusetts had asserted her claim by exercising a sort of supervision over those who had already gone to Connecticut; but in October John Winthrop, Jr., the Reverend Hugh Peters, and Henry Vane arrived from England with authority from the lords and gentlemen to push their claim, and Winthrop actually bore a commission as governor of the entire territory, which included Connecticut. It is hardly possible that Hooker and Haynes would have ignored the demands of these agents, and yet to acknowledge Winthrop as their governor would have been to accept a head who was not of their own choosing. In all probability some arrangement was made with Winthrop, according to which the Englishmen's title to the lands was recognized but at the same time the Connecticut settlers were to have full powers of self-government, and the question of a governor was left for the moment undecided, Winthrop confining his jurisdiction to Saybrook, the settlement which he was to promote at the mouth of the river. This agreement was embodied in a commission which was drawn up by the Massachusetts General Court and issued in March, 1636, "on behalf of our said members and John Winthrop, Jr.," and was to last for one year. Who actually wrote this commission we do not know, but the Connecticut men said afterwards that it arose from the desire of the people who removed, because they did not want to go away without a frame of government agreed on beforehand and did not want to recognize "any claymes of the Massachusetts jurisdiction over them by vertew of Patent." Apparently the people going to Connecticut wanted to get as far away from Massachusetts as possible.

Armed with their commission, in the summer of 1636, members of the Newtown church to the number of about one hundred persons, led by Thomas Hooker, their pastor, and Samuel Stone, his assistant, made a famous pilgrimage under summer skies through the woods that lay between Massachusetts and the Connecticut River. Bearing Mrs. Hooker in a litter and driving their cattle before them, these courageous pioneers, men, women, and children, after a fortnight's journeying, reached Hartford, the site of their future home, already occupied by those who had foregathered there in number larger even than those who had newly arrived. At about the same time, William Pynchon and others of Roxbury, acting from similar motives, took the same course westward, but instead of continuing down the Connecticut River, as the others had done, stopped at its banks and made their settlement at Agawam (Springfield), where they built a warehouse and a wharf for use in trade with the Indians. The lower settlements, Hartford, Wethersfield, and Windsor, became agricultural communities; but Springfield, standing at the junction of Indian trails and river communication, was destined to become the center of the beaver trade of the region, shipping furs and receiving commodities through Boston, either in shallops around the Cape or on pack-horses overland by the path the emigrants had trod. Pynchon's settlement was one of the towns named in the commission and, for the first year after it was founded, joined with the others in maintaining order in the colony.

The commission government came to an end in March, 1637, and there is reason to think that during the last month, an election of committees took place in Hartford, Wethersfield, and Windsor, which would show that the Connecticut settlers were exercising the privilege of the franchise more than a year before Hooker preached his famous sermon declaring that the right of government lay in the people. There also is some reason to think that the leaders were still undecided whether or not to come to an agreement with the English lords and gentlemen and to put themselves under the latter's jurisdiction. But as Winthrop's commission expired at the end of a year and no new governor was appointed—the English Puritans having become absorbed in affairs at home—the Connecticut colony was thrown on its own resources and compelled to set up a government of its own. Pynchon at Springfield now cast in his lot with Massachusetts, and from this time forward Springfield was a part of the Massachusetts colony, but the men of Connecticut, disliking Pynchon's desertion, determined to act for themselves. On May 31, 1638, Hooker preached a sermon laying down the principles according to which government should be established; and during the six months that followed, the court, consisting of six magistrates and nine deputies, framed the Fundamental Orders, the laws that were to govern the colony.

This remarkable document, though deserving all the encomiums passed upon it, was not a constitution in any modern sense of the word and established nothing fundamentally new, because the form of government it outlined differed only in certain particulars from that of Massachusetts and Plymouth. It was made up of two parts, a preamble, which is a plantation covenant like that signed in the cabin of the Mayflower, and a series of laws or orders passed either separately or together by the court which drafted them. This court was a lawmaking body and it made public the laws when they were passed. That this body of laws or, as we may not improperly call it, this frame of government was ratified, as Trumbull says, by all the free planters assembled at Hartford on January 14, 1639, is not impossible, though such action would seem unnecessary as the court was a representative body, and unlikely as the time of year was not favorable for holding a mass-meeting at Hartford. Later courts never hesitated to change the articles without referring the changes to the planters. The articles simply confirmed the system of magistrates and deputies already in existence and added provisions for the election of a governor and deputy governor—who had not hitherto been chosen because of doubts regarding the jurisdiction of the English lords and gentlemen.

In matters of detail the Connecticut system differed from that of Massachusetts in three particulars: it imposed no religious test for those entitled to vote, but required only that the governor be a church member, though it is probable that in practice only those would be admitted freemen who were covenanted Christians; it gave less power to the magistrates and more to the freemen; and it placed the election of the governor in the hands of the voters, limiting their choice only to a church member and a former magistrate, and forbidding reëlection until after the expiration of a year. Later the qualifications of a freeman were made such that only about one in every two or three voted in the seventeenth century; the powers of the magistrates were increased; and the governor was allowed to succeed himself. Connecticut was less democratic than Rhode Island in the seventeenth century and, as the years went on, fewer and fewer of the inhabitants exercised the freeman's privilege of voting for the higher officials. By no stretch of the imagination can the political conditions in any of the New England colonies be called popular or democratic. Government was in the hands of a very few men.

Two more settlements remain to be considered before a survey of the foundations of New England can be called complete. When the Reverend John Wheelwright, the friend of Anne Hutchinson, was driven from Massachusetts and took his way northward to the region of Squamscott Falls where he founded Exeter, he entered a territory of grants and claims and rights of possession that render the early history of New Hampshire a tangle of difficulties. Out of a grant to Gorges and Mason of the stretch of coast between the Merrimac and the Kennebec in 1622, and a confirmation of Mason's right to the region between the Merrimac and the Piscataqua, arose the settlement of Strawberry Bank, or Portsmouth, and accompanying it a controversy over the title to the soil that lasted throughout the colonial period. Mason called his territory New Hampshire; Gorges planned to call the region that he received New Somersetshire; and both designations took root, one as the name of a colony, the other as that of a county in Maine. At an earlier date, merchants of Bristol and Shrewsbury had become interested in this part of New England and had sent over one Edward Hilton, who some time before 1627 began a settlement at Dover. The share of the Bristol merchants was purchased in 1633 by the English lords and gentlemen already concerned in the Connecticut settlement, for the purpose, it may be, of furnishing another refuge in New England, should conditions at home demand their withdrawal overseas. But nothing came of their purchase except an unfortunate controversy with Plymouth colony over trading boundaries on the Kennebec.

The men established on this northern frontier were often lawless and difficult to control, of loose habits and morals, and intent on their own profit; and the region itself was inhospitable to organized and settled government. Yet out of these somewhat nebulous beginnings, four settlements arose—Portsmouth (Masonian and Anglican), Dover (Anglican and Puritan), Exeter and Hampton (both Puritan), each with its civil compact and each an independent town. The inhabitants were few in number, and "the generality, of mean and low estates," and little disposed to union among themselves. But in 1638-1639, when Massachusetts discovered that one interpretation of her charter would carry her northern boundary to a point above them, she took them under her protecting wing. After considerable debate this jurisdiction was recognized and the New Hampshire and Maine towns were brought within her boundaries. Henceforth, for many years a number of these towns, though in part Anglican communities and never burdened with the requirement that their freemen be church members, were represented in the general court at Boston. Nevertheless the Mason and Gorges adherents—whose Anglican and pro-monarchical sympathies were hostile to Puritan control and who were supported by the persistent efforts of the Mason family in England—were able to obtain the separation of New Hampshire from Massachusetts in 1678. Maine, however, remained a part of the Bay Colony to the end of the colonial period.