Down to this time the supreme control over colonial affairs had been in the hands of the king and his privy council, and the Parliament had not disputed it.  In 1624 they had grumbled at James I.’s high-handed suppression of the Virginia Company, but they had not gone so far as to call in question the king’s supreme authority over the colonies.  In 1628, in a petition to Charles I. relating to the Bermudas, they had fully admitted this royal authority.  But the fall of Charles I. for the moment changed all this.  Among the royal powers devolved upon Parliament was the prerogative of superintending the affairs of the colonies.  Such, at least, was the theory held in England, and it is not easy to see how any other theory could logically have been held; but the Americans never formally admitted it, and in practice they continued to behave toward Parliament very much as they had behaved toward the crown, yielding just as little obedience as possible.  When the Earl of Warwick’s commissioners in 1644 seized upon a royalist vessel in Boston harbour, the legislature of Massachusetts debated the question whether it was compatible with the dignity of the colony to permit such an act of sovereignty on the part of Parliament.  It was decided to wink at the proceeding, on account of the strong sympathy between Massachusetts and the Parliament which was overthrowing the king.  At the same time the legislature sent over to London a skilfully worded protest against any like exercise of power in future.  In 1651 Parliament ordered Massachusetts to surrender the charter obtained from Charles I. and take out a new one from Parliament, in which the relations of the colony to the home government should be made the subject of fresh and more precise definition.  To this request the colony for more than a year vouchsafed no answer; and finally, when it became necessary to do something, instead of sending back the charter, the legislature sent back a memorial, setting forth that the people of Massachusetts were quite contented with their form of government, and hoped that no change would be made in it.  War between England and Holland, and the difficult political problems which beset the brief rule of Cromwell, prevented the question from coming to an issue, and Massachusetts was enabled to preserve her independent and somewhat haughty attitude. [Sidenote:  Fall of Charles I. brings up the question as to supremacy of Parliament over the colonies]

During the whole period of the Confederacy, however, disputes kept coming up which through endless crooked ramifications were apt to end in an appeal to the home government, and thus raise again and again the question as to the extent of its imperial supremacy.  For our present purpose, it is enough to mention three of these cases:  1, the adventures of Samuel Gorton; 2, the Presbyterian cabal; 3, the persecution of the Quakers.  Other cases in point are those of John Clarke and the Baptists, and the relations of Massachusetts to the northeastern settlements; but as it is not my purpose here to make a complete outline of New England history, the three cases enumerated will suffice.