It is well for us to bear in mind the foregoing considerations as we deal with the history of the short-lived New England Confederacy.  The story is full of instances of an intolerant and domineering spirit, especially on the part of Massachusetts, and now and then this spirit breaks forth in ugly acts of persecution.  In considering these facts, it is well to remember that we are observing the workings of a system which contained within itself a curative principle; and it is further interesting to observe how political circumstances contributed to modify the Puritan ideal, gradually breaking down the old theocratic exclusiveness and strengthening the spirit of religious liberty.

Scarcely had the first New England colonies been established when it was found desirable to unite them into some kind of a confederation.  It is worthy of note that the separate existence of so many colonies was at the outset largely the result of religious differences.  The uniformity of purpose, great as it was, fell far short of completeness. [Sidenote:  Existence of so many colonies due to slight religious differences]

Could all have agreed, or had there been religious toleration in the modern sense, there was still room enough for all in Massachusetts; and a compact settlement would have been in much less danger from the Indians.  But in the founding of Connecticut the theocratic idea had less weight, and in the founding of New Haven it had more weight, than in Massachusetts.  The existence of Rhode Island was based upon that principle of full toleration which the three colonies just mentioned alike abhorred, and its first settlers were people banished from Massachusetts.  With regard to toleration Plymouth occupied a middle ground; without admitting the principles of Williams, the people of that colony were still fairly tolerant in practice.  Of the four towns of New Hampshire, two had been founded by Antinomians driven from Boston, and two by Episcopal friends of Mason and Gorges.  It was impossible that neighbouring communities, characterized by such differences of opinion, but otherwise homogeneous in race and in social condition, should fail to react upon one another and to liberalize one another.  Still more was this true when they attempted to enter into a political union.  When, for example, Massachusetts in 1641-43 annexed the New Hampshire townships, she was of necessity obliged to relax in their case her policy of insisting upon religious conformity as a test of citizenship.  So in forming the New England Confederacy, there were some matters of dispute that had to be passed over by mutual consent or connivance. [Sidenote:  It led to a notable attempt at federation]