When they accused him of being an enemy of Protestants he produced the proclamation of Charles II., deposing him from the government on account of his adherence to them.
Finally, he exhibited a declaration in his behalf signed by many of the Puritan emigrants from Virginia, among whom were William Durand, their elder, and James Cox and Samuel Puddington, the two burgesses from Providence in the assembly of 1650.[33] Nevertheless, Baltimore played a losing game.

At heart the Puritans in England were unfriendly to him because of his religion; and, when persistent rumors reached Maryland that Baltimore's patent was doomed, some of the men of Providence appeared in England and urged that it be revoked.[34] At length, October 3, 1650, Parliament passed an ordinance authorizing the Council of State to reduce to obedience Barbadoes, Antigua, Bermudas, and "Virginia," the last being a term which in England was often used to include Maryland.

Baltimore struggled hard to have Maryland left out of the instructions drawn up afterwards by the Council of State; but though he was apparently successful, a descriptive phrase including his province was inserted, for the commissioners, Curtis, Claiborne, and Bennett, with an armed fleet, were instructed "to use their best endeavors to reduce _all the plantations within the Bay of Chesopiack_ to their due obedience to the Parliament of England."[35] After the commissioners had reduced Virginia, they found even less resistance in Maryland.

The commissioners landed at St.Mary's, and, professing their intention to respect the "just rights" of Lord Baltimore, demanded that Stone should change the form of the writs from the name of Lord Baltimore to that of Parliament.

Stone at first declined to comply, and the commissioners, March 29, 1652, put the government into the hands of a council of leading Protestants.