This article is excerpted from Conceived in Liberty, volume 1, chapter 37, "The Restoration Crisis in New England." An MP3 audio file of this article, narrated by Floy Lilley, is available for download.

The Restoration of the Crown in May 1660 was a fateful event for New England. The destruction of the Puritan Revolution had ended, and the home country could now turn its full attention to the state of the American colonies. From the royal point of view the Southern colonies were in satisfactory order: Virginia, always of royal sympathies, had already restored the royal Governor Berkeley to his post; and the Calverts had quickly returned to control of Maryland.

But in the north, the New England colonies appeared chaotic. Not one colony had a royal governor; all were self-governing, and three – Rhode Island, New Haven, and Connecticut – didn’t even have a proper charter. Connecticut and New Haven were completely without a charter, and Rhode Island’s perfunctory charter had been granted by the Commonwealth Parliament and thus could hardly be deemed valid by the restored Crown. And though Charles II in his Declaration of Breda, preceding the Restoration, had pledged religious liberty, none of the Puritan or dissenting colonies of New England anticipated warm treatment.

Neither were the New England colonies reassured by the English condemnation of those implicated in the death of Charles I. Of those implicated 14, including Henry Vane and Hugh Peter, were executed, 25 committed to life imprisonment, and many others exiled or excluded from public office. Two of the regicides, Whalley and Goffe, escaped to New England, where they were protected and became the objects of constant complaint by the English government, which was convinced that the two were plotting to restore the Commonwealth.

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The news of the Restoration was, indeed, received as a calamity in New England, signifying at the least the end of the Puritan republic, which had treated these colonies almost as self-governing allies. Typical of New England’s response to the Restoration was the comment of Roger Williams: "The bloody whore is not yet drunk enough with blood of the Saints." But the New England colonies prudently decided to recognize the Restoration government: Rhode Island in October 1660, Connecticut and New Haven in March and June of 1661, and Massachusetts trailing them all in August 1661.

The first order of business for the three New England charterless colonies was to preserve their self-government by obtaining royal charters. Connecticut, one of the three, determined to seize the occasion to annex some or most of the territory of its neighbors. John Winthrop Jr. was sent to London as Connecticut’s agent to try to annex all of Rhode Island, New Haven, and even New Netherland to the west, still in the hands of the Dutch. If not all of Rhode Island, then Connecticut at least tried to seize the Narragansett Country, about one-third of present Rhode Island – the territory to the southwest of Warwick and west of Narragansett Bay.

Winthrop was particularly eager to acquire the Narragansett Country as he was a leading partner of the Atherton Company of Massachusetts, speculators whose arbitrary claims to the land were backed by Connecticut. This backing was quite understandable: the Atherton Company had been recently formed, in 1659, and had engaged in a spurious purchase of the choicest areas of the Narragansett Country, near Boston Neck, from the sachem of the Narragansett Indians. Winthrop had then proceeded to use his power as governor of Connecticut to add greatly to the possessions of himself and his partners. In the fall of 1660 Winthrop induced the New England Confederation to order the Narragansett Indians to pay Connecticut a huge fine in wampum in compensation for various disturbances in the border regions. The gracious alternative offered the Indians was to mortgage the entire Narragansett Country to the Connecticut government. Captain Humphrey Atherton, a major partner of the Atherton Company, now in turn graciously paid the Indian fine, provided that Connecticut transfer the mortgage of the Narragansett Country to the company. By treading this path of chicanery and coercion, the Atherton Company managed to acquire a claim – unrecognized by Rhode Island – to the Narragansett Country of Rhode Island. Only Connecticut jurisdiction guided by the company’s own Winthrop could guarantee the land to the company.

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Connecticut’s designs on New Haven were also made clear before Winthrop arrived in London. It had sent an arrogant message to the latter colony in early 1661, asserting "our own real and true right, to those parts of the country where you are seated, both by conquest, purchase and possession."

Winthrop managed, by judicious distribution of money in London, to obtain for Connecticut a royal charter in May 1662. The charter confirmed Connecticut’s powers of self-government and left its political structure intact, except for restricting the franchise completely to freemen of the colony. The royal charter granted to Connecticut all land west of Narragansett Bay and south of Massachusetts. By this, Rhode Island territory was reduced to the tiny area of existing settlement, and New Haven Colony – whose existence was not even mentioned by Connecticut in its negotiations at London – was wiped out altogether.

It is quite probable that the new English government, in the confusion of the day, had never heard of New Haven Colony, and that its grant of New Haven’s territory to Connecticut was entirely unwitting. The problem was that New Haven, a fading colony with an economy in decline, felt itself too poor to afford the expense of maintaining an agent in London, and it believed that either Connecticut or Massachusetts, its brothers in the New England Confederation, would look after its interests. Very fortunately, Rhode Island did have an agent in London to speak up for its interest. Dr. John Clarke had remained there after Roger Williams’s return to Rhode Island years before. When Charles II assumed the throne, Clarke had urged a new charter for Rhode Island, stressing its great principle of "soul liberty," or freedom of conscience, and shrewdly emphasizing the similarity of that principle to Charles’s views in his Declaration of Breda.

Now, as soon as Clarke heard of the aggressive Connecticut charter gained by Winthrop, he appealed to the king for a charter and for review of the Connecticut document, which had "injuriously swallowed up one half of our colony." In response, Edward Hyde Clarendon, the lord chancellor, blocked the Connecticut charter and the dispute raged between Winthrop and Clarke, with Winthrop continuing to insist that the Narragansett lands belonged to Connecticut.

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Finally they submitted the dispute to five arbitrators, who awarded the entire Narragansett Country to Rhode Island; the Pawcatuck River was to be the latter’s western boundary, as in the original Rhode Island patent in 1644. The award also provided, however, that the Atherton Company was free to shift the jurisdiction over its land to Connecticut. John Winthrop Jr.’s personal property on Fishers Island, on the boundary, was also carefully given to Connecticut. With Winthrop and Clarke both accepting the settlement in April 1663, Winthrop now joined in support of a royal charter for Rhode Island. Finally, in July 1663, the Crown granted Rhode Island its charter as a self-governing colony, including the Narragansett land.

Particularly remarkable in the charter was the explicit guarantee of religious freedom for Rhode Island:

No person within the said colony was to be anywise molested, punished, disquieted or called in question for any differences in opinion in matters of religion, and do not actually disturb the civil peace.

Furthermore, Rhode Island was protected from encroachment by Massachusetts by guarantees of freedom to trade with the Bay Colony. In general, the governmental changes made by the new royal charter were minor: the president’s title was changed to governor, and the number of assistants or magistrates expanded from four to ten. The new charter, however, did cause the removal of the important nullification check on central government power in Rhode Island, by rescinding the law requiring a majority of towns to approve the laws of the General Court. Two years later the Crown restricted democracy further by requiring that suffrage in Rhode Island, as well as in the rest of New England, be limited to those with "competent estates."

The Narragansett land dispute was far from over. As soon as Winthrop had concluded his agreement with Clarke in April, he joyfully sailed for home, convinced that he had outsmarted Rhode Island. By the agreement the Atherton Company was recognized as the owners of the Narragansett lands and it was granted a free choice of jurisdiction. Winthrop had no doubt which path his associates would choose. As soon as he landed, Winthrop and his partners voted to shift jurisdiction of the Narragansett Country from Rhode Island to Connecticut and Connecticut eagerly accepted the gift. But, in the meanwhile, in the course of drafting the Rhode Island charter, Clarke had shrewdly neglected to include any mention of a free option to the Atherton Company. Thus, Rhode Island obtained a charter with unconditional jurisdiction over the Narragansett lands.

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But if Dr. Clarke did a superb job of winning rights for Rhode Island in the turbulent years following the Restoration, hapless New Haven suddenly found itself blotted from the map. Here was a treacherous blow indeed from its neighbor colony, and a clear violation of the terms of the New England Confederation.

In addition to treachery without, New Haven was suffering increasing opposition within – rebellion against its extreme theocratic and oligarchic rule. The opposition denounced the severe limitations on suffrage and longed to join the more liberal and prosperous Connecticut. Francis Browne, for example, denounced the New Haven government and magistrates and refused to obey laws not in conformity with the laws of England.

When news of the royal grant of New Haven to Connecticut arrived in the fall of 1662, Connecticut issued an ultimatum to New Haven Colony to surrender its jurisdiction to it. The colony refused, but town after town now took advantage of the opportunity to shift its allegiance from New Haven to Connecticut. First came Southold on Long Island and then part or all of Stamford, Greenwich, and Guilford. By the end of 1662, the jurisdiction of New Haven had shrunk to a fraction – to its hard core. Only the towns of New Haven proper, Milford, and Branford remained.

The core of New Haven, headed by Governor William Leete and Rev. John Davenport, remained adamant. The freemen of the colony voted to keep its independence, and to appeal the decision to the king and ask for a charter for the colony. New Haven then took its case to the New England Confederation, charging Connecticut with gross violation of its terms. In September 1663 the commissioners of the United Colonies voted in favor of New Haven and its continued independence. Connecticut, however, blithely ignored the verdict of the commissioners and continued to demand unconditional submission. New Haven, for its part, took heart in the winter of 1664 when the Crown’s order to the colonies enjoining enforcement of the Navigation Acts included New Haven in its address. This seemed to accord implicit royal recognition of New Haven’s autonomy. Even the defection of the town of Milford to Connecticut could not dampen New Haven’s hopes for survival.

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But in 1664 the crisis reached its culmination. The king took the first step down the path of ending the right of self-government in New England by sending four commissioners to New England in mid-1664 to try to enforce the navigation laws, settle disputes, and generally begin the process of taking over the colonies. In the meanwhile, in March, the king decided to give to his brother James, the Duke of York, the entire huge area of New Netherland, which England was in the process of seizing from the Dutch: from the Connecticut River all the way south to Delaware Bay – virtually the entire middle area between New England and the Southern colonies of Chesapeake Bay. For good measure, James was also granted all of central and eastern Maine, from the Kennebec River east to St. Croix on the Canadian border.

The huge grant to the Duke of York startled Connecticut, for all of Long Island now belonged to the duke. In 1650 New England had come to an amicable agreement with the Dutch for partitioning Long Island: three-quarters of the island east of Oyster Bay went to Connecticut or New Haven, and Dutch sovereignty was virtually limited to Long Island areas that now are Nassau County and part of New York City. Now, suddenly, the Long Island towns had been transferred to the Duke of York. But far more dangerous was the fact that James was now granted all land west of the Connecticut River. This meant the virtual eradication of the colony of Connecticut; all the significant towns in the colony, except New London, were located west of this river. Its charter thus completely negated, and being anxious to present the royal commission with a fait accompli, Connecticut again demanded total submission from New Haven and sent its agents to that colony to take over the government.

The other colonies also wanted to settle matters as quickly as possible. The commissioners of the United Colonies reversed their stand in September and endorsed Connecticut’s appropriation of New Haven. Finally, in November the royal commissioners agreed and decided that all the New Haven area belonged to Connecticut.

The blow was final. The Crown had decided. In December 1664 the New Haven General Court surrendered but under bitter protest to the last, denouncing the injustice imposed by Connecticut. New Haven Colony was ended, and the towns became part of the considerably more liberal colony of Connecticut.

The most extreme and rigid Puritan theocracy in New England was thus no more. The Reverend John Davenport, founder and spiritual chief of New Haven, moved to the ministry of First Boston Church, there to end his days in bitter controversy, as the foremost and most relentless enemy of the Half-Way Covenant.

As for Branford’s zealous minister, Rev. Abraham Pierson, he had led his flock there from Southampton, Long Island, two decades before, when that town had decided to join the lax rule of Connecticut. He was not now prepared to give up the strict theocratic ideal, and so he moved his flock once more, this time to found another theocratic settlement in former Dutch territory at New Ark, on the banks of the Passaic River.

With New Haven seized by Connecticut, the New England Confederation came to a virtual end. Although it formally existed for 20 more years, its annual meetings ceased and it no longer played a significant role in New England affairs.

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