Now it should probably be mentioned that England didn’t exactly turn a blind eye to the fact that the colonies in New England were pretty much functioning as independent governments. It was just that for awhile the were pretty busy with other things, such as the English Civil War, which tended to divert their attention. However, when King Charles II took the throne on 1660, work began to better bring the colonies under control. From the English standpoint, its colonies existed only to ship needed resources to England. As such, between 1660 and 1673, the English parliament passed a series of what became known as the Navigation Acts, which required the colonies to only export and import goods to and from England, which could only be carried by English owned ships crewed by a majority of English sailors, and restricted trade between the colonies. These acts rather sucked for all of the English colonies, in that it restricted trade, raising costs and lowering profits, but they were especially unpopular in New England.
Over the past several decades New England had increasingly become a center of manufacturing; especially textiles, leather goods, and ironware; and merchant shipping in the New World. While this was pretty good for the colonies, it was bad for England, which formerly made a lot of money from this trade. The Navigation Acts were meant to ensure England continued to profit from its colonies. However, instead of kowtowing as they were supposed to, many of the New England ship owners just did what they had always done, trading with whomever they damn well pleased, just now technically illegally. As one can probably imagine, this infuriated the English, who demanded that the colonial governments do something about it, which they of course promised to do, though also of course totally didn’t do. Things only became worse after King Philip’s War, with many of the New England colonists feeling England had failed to help them in their time of need, which they totally had, hoping that the devastation of the New England colonies would fix the issue. The fact that the Puritans had been staunchly opposed to the royalists during the English Civil War and were actively also thumbing their noses at demands that they not persecute everyone who wasn’t Puritan didn’t help matters any either.
Things finally came to a head in 1685 when Charles II died and his brother James II came to the throne. Lacking the patience of his brother, James II just said fuck it and annulled the charters of all of the New England colonies, placing them all under the administration of Edmund Andros, the appointed governor of New York. The new Dominion of New England included New Hampshire, Massachusetts, Rhode Island, Connecticut, New York, and New Jersey. Andros quickly ended the elected assemblies, enforced the Navigation Acts, promoted the Anglican church, and threatened to not recognize any of the land titles granted by the colonial governments. As one can imagine, this pissed off pretty much everyone it was possible to piss off, and a significant amount of unrest began to manifest, to which Andros responded by banning town meetings and threats of bringing in the English army. Growing conflict between the colonists and French armed natives on the frontier only made the situation worse.
It's hard to say what might have happened next if things had continued going as they were, but we’ll never know because in 1688 the Glorious Revolution took place, wherein James II was deposed and replaced by King William III. When word of this reached the colonies in early 1689, mobs formed in a number of cities and towns which seized and imprisoned Andros and his flunkies. The former colonial assemblies were reconvened and took back control. When word of this reached the newly crowned King William III, he was much less concerned than his predecessors. Both he and the New England colonists had bigger fish to fry, namely a growing war with France. As such, they agreed to a compromise. All of the colonies could still have elected assemblies as long as they had governors appointed by the king and laws limiting rights and privileges to only Puritans were revoked. In return, at least unofficially, England would not fully enforce the Navigation Acts on New England, which was less pertinent given the growing conflict with France was already curtailing the New England trade. The compromise worked, and though it did cause a bit of a panic amongst the Puritan majority, which became part of the cause of the infamous Salem Witch Trials of 1692, it did end the crisis, at least for the foreseeable future.
