They could assume high prerogatives, arrogate to themselves divine favour and protection, threaten divine judgments on their adversaries, boast of courage and power; but they knew that in a trial of strength on the battlefield their strength would prove weakness, and that they would be swept from power, and perhaps proscribed and oppressed by the very victims of their intolerance.

The "breaking in upon ancient unanimity" was but the declining power of a disloyal Church and State Government of one denomination.

A second cause hinted at by Dr.Palfrey why the rulers of Massachusetts Bay did not resort to arms at this time was, that "_the rest of New England was more or less inclined to the adverse interest_." They could command no rallying watchword to combine the other New England colonies against the King, such as they were enabled to employ the following century to combine all the American colonies.
"The rest of New England" had found that in the King and Council was their only effectual protection against the aggressions and domination of the rulers of Massachusetts Bay, who denied all right of appeal to the Crown, and denied the right of the Crown to receive and decide upon such appeals.

These rulers not only encroached upon the lands of neighbouring colonies, but interfered with their exercise of religious toleration.[204] The extinction of the pretensions to supremacy and monopoly of power and trade by the rulers of Massachusetts Bay, was the enfranchisement of the other New England Colonies to protection against aggression, and of four-fifths of the male inhabitants of Massachusetts itself to the enjoyment of equal civil and religious liberty.
I think therefore that "ambitions and mean longings," and even "venality," had quite as much to do on the part of those who wished to perpetuate the government of disloyalty, proscription, and persecution as on the part of those who desired to "render unto Caesar the things that are Caesar's," and to place the Government of Massachusetts, like that of the other New England Colonies, upon the broad foundation of equal and general franchise and religious liberty.
But to return from this digression.

After "the fall of the Charter," November, 1684, the Congregationalists of Massachusetts Bay continued their government for two years, as if nothing had happened to their Charter; they promptly proclaimed and took the oath of allegiance to James the Second; and two years afterwards sent the celebrated Increase Mather as agent to England, to thank the King for the Proclamation of Indulgence, which trampled on English laws, and cost the King his throne, to pray for the restoration of the Charter, and to accuse and pray for the removal of the King's obnoxious Governor-General of New England, Sir Edmund Andros.