Throughout New England as a whole, the daily routine of life was pursued without regard to the particular form of government established in Boston. In Massachusetts the election of deputies stopped, but in other respects the town meetings carried on their usual business. In other colonies no changes whatever took place. Men tilled the soil, went to church, gathered in town meetings, and ordered their ordinary affairs as they had done for half a century. The seaports felt the change more than did the inland towns, for the enforcement of the navigation acts interfered somewhat with the old channels of trade and led to the introduction of a court of vice-admiralty which Dudley held for the first time in July to try ships engaged in illicit trade. Over the forts and the royal offices fluttered a new flag, bearing a St. George's cross on a white field, with the initials J. R. and a crown embroidered in gold in the center of the cross, that same cross which Endecott had cut from the flag half a century before. To many the new flag was the symbol of anti-Christ, and Cotton Mather judged it a sin to have the cross restored; but others felt with Sewall, the diarist, who said of the fall of the old government: "The foundations being destroyed, what can the righteous do?"

Perhaps the greatest innovation—in any case, the novelty that aroused the largest amount of curiosity and excitement—was the service according to the Book of Common Prayer, held at first in the library room of the Town House, and afterwards by arrangement in the South Church, and conducted by the Reverend Robert Ratcliffe in a surplice, before a congregation composed not only of professed Anglicans but also of many men of Boston who had never before seen the Church of England form of worship. The Anglican rector, by his somewhat unfortunate habit of running over the time allowance and keeping the waiting Congregationalists from entering their own church for the enjoyment of their own form of worship, caused almost as much discontent as did the dancing-master of whom the ministers had complained the year before, who set his appointments on Lecture days and declared that by one play he could teach more divinity than Mr. Willard or the Old Testament. Other "provoking evils" show that not all the breaches in the walls were due to outside attacks. A list of twelve such evils was drawn up in 1675, and the crimes which were condemned, and which were said to be committed chiefly by the younger sort, included immodest wearing of the hair by men, strange new fashions of dress, want of reverence at worship, profane cursing, tippling, breaking the Sabbath, idleness, overcharges by the merchants, and the "loose and sinful habit of riding from town to town, men and women together, under pretence of going to lectures, but really to drink and revel in taverns." The law forbidding the keeping of Christmas Day had to be repealed in 1681. Mrs. Randolph, when attending Mr. Willard's preaching at the South Church, was observed "to make a curtsey" at the name of Jesus "even in prayer time"; and the colony was threatened with "gynecandrical or that which is commonly called Mixt or Promiscuous Dancing," and with marriage according to the form of the Established Church. The old order was changing, but not without producing friction and bitterness of spirit. The orthodox brethren stigmatized Ratcliffe as "Baal's priest," and the ministers from their pulpits denounced the Anglican prayers as "leeks, garlick, and trash." The upholders of the covenant were convinced that already "the Wild Beasts of the Field" were assailing the colony.

Randolph journeyed on horseback twice to Rhode Island, and once to Connecticut, serving his writs upon those colonies. Rhode Island agreed willingly enough to surrender her charter without a suit, but the authorities of Connecticut, knowing that the time for the return of the writ had expired, gave no answer, debating among themselves whether it would not be better, if they had to give in, to join New York rather than Massachusetts. Randolph attributed their hesitation to their dislike of Dudley, for whom he had begun to entertain an intense aversion. He charged Dudley with connivance against himself, interference with his work, appropriation of his fees, and too great friendliness toward the old faction in Boston. Before the provisional government had come to an end, he was writing home that Dudley was a "false president," conducting affairs in his private interest, a lukewarm supporter of the Anglican church, a backslider from his Majesty's service, turning "windmill-like to every gale." Such was Dudley's fate in an era of transition—hated by the old faction as an appointee of the Stuarts and by Randolph as a weak servant of the Crown. Writing in November, Randolph longed for the coming of the real governor, who would put a check upon the country party and bring to an end the time-serving and trimming of a president whom he deemed no better than a Puritan governor.

The new Governor-General, who entered Boston harbor in the Kingfisher on December 19, 1686, was Sir Edmund Andros, a few years before the Duke of York's Governor for the propriety of New York. Andros at this time was forty-nine years old; he was a soldier by training and a man of considerable experience in positions requiring executive ability. His career had been an honorable one, and no charges involving his honesty, loyalty, or personal conduct had ever been entered against him. When he was in New York, he had been brought on several occasions into contact with the Massachusetts leaders, and though their relations had never been sympathetic, they had not been unfriendly. While in England from 1681 to 1686, he had been freely consulted regarding the best method of dealing with the problems in America and had shown himself in full accord with that policy of the Lords of Trade which attempted to consolidate the northern colonies into a single government for the execution of the acts of trade and defense against the encroachments of the French and Indians. He was probably fully aware of the difficulties that confronted the new experiment, but as a soldier he was ready to obey orders. His natural disposition and military training rendered him impatient of obstacles, and his unfamiliarity with any form of popular government—for New York had been controlled by a governor and council only—made extremely uncertain his success in New England, where affairs had been managed by the easy-going, dilatory method of debate and discussion. As a disciplinarian, he could not appreciate the New Englander's fondness for disputation and argument; as a soldier, he was certain to obey to the full the letter of his instructions; and, as an Anglican, he was likely to favor the church and churchmen of his choice. He was not a diplomat, nor was he gifted with the silver tongue of oratory or the spirit of compromise. He came to New England to execute a definite plan, and he was given no discretion as to the form of government he was to set up. He and his advisory council were to make the laws, levy taxes, exercise justice, and command the militia. He was not allowed to call a popular assembly or to recognize in any way the highly prized institutions of the colony.

On December 20, Andros, his officers, and guard, clad in the brilliant uniforms of soldiers of the British establishment, landed at Leverett's wharf and marched through the local militia up King's Street to the Town House, where he read his commission and administered the oaths. Except for the royal commissioners of 1664, no British officer or soldier had hitherto set foot on the streets of Boston. Redcoats had been sent to New York and Virginia, but never before had they appeared in New England, and this visible sign of British authority must have seemed to many ominous for the future.

Andros's early impressions of what he saw were not flattering to the colony. He found the people still suffering from the devastating effects of the late war and further harassed by bad harvests, disasters at sea, and two serious fires which had recently done much damage in the city. He found the fortifications in bad repair, almost all the gun-carriages unserviceable, no magazines of powder or other stores of war, no small arms, except a few old matchlocks, and those unsizable and in poor condition, no storehouses or accommodations for officers or soldiers, and no adequate ramparts or redoubts.

Now the work that Andros had come over to perform, and that which was most important in his eyes, was the defense of New England against the French. The contest between the two nations for control of the New World had already begun. The territory between Hudson Bay and the St. Lawrence and that between the Penobscot and the St. Croix were already in dispute, and New Englanders had taken their part in the conflict. When Governor of New York, Andros had become aware of the French danger, and his successor Dongan had proved himself capable of holding the Iroquois Indians to their allegiance to the English and of extending the beaver trade in the Mohawk Valley. But at this juncture reports kept coming in of renewed incursions of the French, led by the Canadian nobility, into the regions south of Lakes Erie and Ontario, and of new forts on territory that the English claimed as their own. There was increasing danger that the French would embroil the Indians of the Five Nations and, by drawing them into a French alliance, threaten not only the fur trade but the colonies themselves. The French Governor, Denonville, declared that the design of the King his master was the conversion of the infidels and the uniting of "all these barbarous people in the bosom of the Church"; but Dongan, though himself a Roman Catholic, saw no truth in this explanation and demanded that the French demolish their forts and retire to Canada, whence they had come. Just as this quarrel with the French threatened to arouse the Indians in northwestern New York, so it threatened to arouse, as eventually it did arouse, the Indians along the northern frontier of New England. To the authorities in England and to Andros in America, this menace of French aggression was one of the dangers which the Dominion of New England was intended to meet, and the substitution of a single civil and military head for the slow-moving and ineffective popular assemblies was designed to make possible an energetic military campaign.

Andros had no sooner organized his council and got his government into running order than he began to prosecute measures for improving the defenses of the colony. He sent soldiers to Pemaquid to occupy and strengthen the fort there, and himself began the reconstruction of the fortifications of Boston. He turned his attention to Fort Hill at the lower end of the town, erected a palisaded embankment with four bastions, a house for the garrison, and a place for a battery; later he leveled the hill on Castle Island in the harbor, and built there a similar palisade and earthwork and barracks for the soldiers. He took a survey of military stores, made application to England for guns and ammunition, endeavored to put the train-bands of the colony in as good shape as possible, and in 1688 went to Pemaquid to inspect the northern defenses as far as the Penobscot. He kept in close touch with Governor Dongan, and promised to send him, as rapidly as he could, men and money in case of a French invasion.

To make his work more effective he took steps to bring Connecticut immediately under his control. Rhode Island had already submitted and had sent its members to sit with the council at Boston. But Connecticut had avoided giving a direct answer, although a third writ of quo warranto had been served upon her, on December 28, 1686. Consequently Andros wrote to the recalcitrant colony, saying that he had been instructed to receive the surrender of the charter. To this letter, the Governor and magistrates of Connecticut replied that they preferred to remain as they were, but that, if annexation was to be their lot, they would be willing to join with Massachusetts, their old neighbor and friend, rather than with New York. Dongan, perplexed by the heavy expenses involved in the military defense of his colony and wishing to have the use of additional revenues, had hoped that he might persuade the Connecticut Government to come under the control of New York, but Connecticut preferred Massachusetts and had stated this preference in her letter. Andros and the Lords of Trade deemed the reply favorable, although in fact it was ingeniously noncommittal, and they took steps to complete the annexation.

On receiving a special letter of instructions from the King, Andros set out in person for Hartford, accompanied by a number of gentlemen, two trumpeters, and a guard of fifteen or twenty redcoats, "with small guns and short lances in the tops of them." He journeyed probably by way of Norwich, crossing the Connecticut River at Wethersfield, where he was met by a troop of sixty cavalry and escorted to Hartford. There, on October 31, 1687, the Governor, magistrates, and militia awaited his coming. Seated in the Governor's chair in the tavern chamber where the assembly was accustomed to meet, he caused his commission to be read, declared the old Government dissolved, selected two of those present as members of his council, and the next day appointed the necessary officials for the colony. Thence he went to Fairfield, New Haven, and New London, commissioning justices of the peace for those counties and organizing the customs service. No resistance was made to his proceedings, though it was generally understood in the colony that the charter itself had been spirited away and hidden in the hollow of an oak tree, henceforth famous as the Charter Oak.